ABL_region234_parser

workflowr

• Summary
• Checks
• Past versions

Last updated: 2024-12-23

Checks: 7 0

Knit directory: duplex_sequencing_screen/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

---

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20200402)

The command set.seed(20200402) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 0a84364

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 0a84364. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    code/archive/
    Ignored:    data/Consensus_Data/.Rhistory
    Ignored:    data/Consensus_Data/Marta_tileseq/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_H_1_3_R1/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_H_1_3_R1/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_H_1_3_R2/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_H_1_3_R2/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_Lo_1_3_R1/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_Lo_1_3_R1/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_Lo_1_3_R2/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_Lo_1_3_R2/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_M_1_3_R1/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_M_1_3_R1/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_M_1_3_R2/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_M_1_3_R2/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_N_1_3_R1/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_N_1_3_R1/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_N_1_3_R2/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_A_N_1_3_R2/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_H_1_3_R1/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_H_1_3_R1/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_H_1_3_R2/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_H_1_3_R2/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_Lo_1_3_R1/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_Lo_1_3_R1/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_Lo_1_3_R2/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_Lo_1_3_R2/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_M_1_3_R1/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_M_1_3_R1/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_M_1_3_R2/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_M_1_3_R2/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_N_1_3_R1/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_N_1_3_R1/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_N_1_3_R2/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_B_N_1_3_R2/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_D0_A_1_3_R1/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_D0_A_1_3_R1/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_D0_A_1_3_R2/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_D0_A_1_3_R2/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_D0_B_1_3_R1/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_D0_B_1_3_R1/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_D0_B_1_3_R2/.DS_Store
    Ignored:    data/Consensus_Data/Marta_tileseq/BR1_D0_B_1_3_R2/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Novogene_lane11/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane11/sample1/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane11/sample2/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane11/sample3/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane11/sample4/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane11/sample7/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane12/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane12/sample1/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane13/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane13/sample1/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane13/sample10/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane13/sample11/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane13/sample12/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane13/sample7/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane13/sample8/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Novogene_lane13/sample9/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane14/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane14/sample10_combined/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane14/sample11/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane14/sample12/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane14/sample13/
    Ignored:    data/Consensus_Data/Novogene_lane14/sample14_combined/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane14/sample14b/
    Ignored:    data/Consensus_Data/Novogene_lane14/sample15/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane14/sample16/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane14/sample17/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane14/sample18/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane14/sample1_combined/
    Ignored:    data/Consensus_Data/Novogene_lane14/sample7/variant_caller_outputs/duplex/
    Ignored:    data/Consensus_Data/Novogene_lane14/sample8/variant_caller_outputs/
    Ignored:    data/Consensus_Data/Novogene_lane14/sample9/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane2/
    Ignored:    data/Consensus_Data/Novogene_lane3/
    Ignored:    data/Consensus_Data/Novogene_lane4/
    Ignored:    data/Consensus_Data/Novogene_lane5/
    Ignored:    data/Consensus_Data/Novogene_lane6/
    Ignored:    data/Consensus_Data/Novogene_lane7/
    Ignored:    data/Consensus_Data/R01Figure/.DS_Store
    Ignored:    data/Consensus_Data/Ranomics_Pooled/
    Ignored:    data/Consensus_Data/archive/
    Ignored:    data/Consensus_Data/novogene_lane15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/egfr/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/egfr/sample_1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/egfr/sample_1/firstrun(lowsequencing)/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/egfr/sample_1/firstrun(lowsequencing)/sscs/
    Ignored:    data/Consensus_Data/novogene_lane15/egfr/sample_1/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/egfr/sample_2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/egfr/sample_2/firstrun(lowsequencing)/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/egfr/sample_2/firstrun(lowsequencing)/sscs/
    Ignored:    data/Consensus_Data/novogene_lane15/egfr/sample_2/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/egfr/sample_2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/ngs/Sample3_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/firstrun(lowsequencing)/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/firstrun(lowsequencing)/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/firstrun(lowsequencing)/sscs/variant_caller_outputs/.empty/
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/firstrun(lowsequencing)/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/firstrun(lowsequencing)/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample12/sscs/
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample13/sscs/
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample14/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample1_combined/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample1_combined/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/duplex/
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample11/
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample1_combined/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample7_combined/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample8_combined/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/variant_caller_outputs/archive/
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample10/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane17/sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/duplex/low_depth/
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/low_seq_depth/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample6/low_seq_depths/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/low_seq_depths/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17/sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17b/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample1 copy 2/
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample1 copy 3/
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample1/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample1/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample2/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/ngs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/l298l/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/nol298l/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/l298l/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/nol298l/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/l298l/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/nol298l/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/l298l/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/nol298l/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample12/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample7/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample11/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample11/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample2/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample2/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample3/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample5/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19b_Sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane22/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample1/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample6/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample7/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample7/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample8/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample8/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane23/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample13/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample13/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample15/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample15/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample17/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample18/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample18/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample19/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample19/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample20/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample20/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample20/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample21/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample21/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample21/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample22/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample22/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample23/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample23/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample24/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample25/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample26/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample26/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample27/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample27/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Sample27/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_10/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_10/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_11/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_11/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_12/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_12/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_13/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_13/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_14/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_14/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_15/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_15/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_15/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_16/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_16/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_17/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_17/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_18/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_18/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_19/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_19/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_19/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_20/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_20/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_20/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_22/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_22/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_22/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_23/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_23/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_23/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_24/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_24/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_24/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_5/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_5/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_5/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_5/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_6/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_6/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_7/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_7/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_8/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_8/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_9/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_9/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane25a/Lane_25a_9/sscs/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane27b/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/L1D0_Sample13_combined/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/L1D0_Sample13_combined/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/L1D0_Sample13_combined/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/L2D0_Sample14_combined/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/L2D0_Sample14_combined/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample1/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample1/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample1/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample11_12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample11_12/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample11_12/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample11_12/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample11_12/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample1_2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample1_2/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample1_2/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample1_2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample3/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane27b/sample3/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample3_4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample3_4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample4/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample4/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample5/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample5_6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample5_6/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample5_6/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample5_6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample7/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample7/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample7_8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample7_8/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample7_8/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample7_8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample8/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample8/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane27b/sample9_10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample9_10/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample9_10/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane27b/sample9_10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28a/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample1/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample1/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28a/sample1/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample10/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample10/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample11/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample11/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample12/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample12/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample14/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample16/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample16/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample17/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample17/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample18/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample18/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample19/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample2/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample2/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample20/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample20/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample20/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample21/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample21/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample21/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample22/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample23/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample24/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample7/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample8/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample9/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28a/sample9/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample10/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample10/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample11/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample11/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample12/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample12/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample13/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample13/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample14/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample14/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample15/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample15/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample16/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample16/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample17/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample17/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample18/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample18/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample19/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample19/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample19/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample20/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample20/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample20/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample21/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample21/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample21/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample22/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample22/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample22/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample23/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample23/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample23/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample24/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample24/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample24/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample9/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28b/sample9/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample1/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample1/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample10/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample10/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample10/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample11/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample11/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample11/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample12/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample12/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample12/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample12/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample13/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample13/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample13/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample14/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample14/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample14/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample15/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample15/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample15/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample16/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample16/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample16/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample17/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample17/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample17/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample17/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample18/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample18/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample18/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample18/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample19/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample19/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample19/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample19/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample2/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample2/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample20/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample20/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample20/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample20/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample21/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample21/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample21/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample21/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample21/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample22/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample22/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample22/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample22/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample23/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample23/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample23/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample23/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample23/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample24/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample24/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample24/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample24/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample3/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample3/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample4/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample4/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample5/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample5/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample6/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample6/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample7/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample7/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample8/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample8/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c/sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample9/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample9/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample9/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c/sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample1/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample1/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample2/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample3/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample4/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample5/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample6/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample6/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample6/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample7/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample8/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old/sample9/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample1/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample1/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample1/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample1/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample10/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample10/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample10/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample11/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample11/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample11/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample12/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample12/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample12/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample12/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample13/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample13/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample13/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample13/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample14/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample14/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample14/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample14/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample15/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample15/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample15/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample15/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample16/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample16/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample16/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample16/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample17/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample17/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample17/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample17/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample18/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample18/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample18/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample18/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample19/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample19/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample19/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample19/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample19/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample2/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample2/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample2/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample20/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample20/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample20/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample20/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample20/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample21/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample21/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample21/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample21/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample21/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample22/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample22/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample22/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample22/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample22/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample23/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample23/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample23/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample23/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample23/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample24/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample24/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample24/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample24/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample24/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample3/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample3/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample3/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample4/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample4/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample4/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample5/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample5/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample5/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample6/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample6/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample6/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample7/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample7/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample7/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample8/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample8/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample8/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample9/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample9/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample9/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_old2/sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_14/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_19/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_20/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_21/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_22/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_23/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_24/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane28c_properlypaired/sample_9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/l298l/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample1/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample10/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample10/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample11/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample11/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample11/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample11/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample12/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample12/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample12/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample13/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample13/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample13/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample14/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample14/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample15/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample15/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample16/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample16/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample17/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample17/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane29a/sample17/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample18/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample18/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample18/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample19/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample19/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample19/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample2/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample2/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample2/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample2/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample2/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample2/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample2/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample2/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample2/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample20/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample20/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample20/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample21/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample21/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample21/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample3/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample4/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample5/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample6/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample6/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample7/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample7/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample8/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample8/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample9/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29a/sample9/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample1/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample10/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample10/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample10/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample11/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample11/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample11/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample2/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/nol298l/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample3/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample4/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample4/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample4/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample5/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample5/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample5/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample6/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample6/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample7/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample7/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample7/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample8/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample8/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample9/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample9/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29b/sample9/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample19_Veri_L1_D0/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample1_Ivan_L1_D6/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample20_Veri_L2_D0/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample21_Veri_L1_D14/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample22_Veri_L2_D14/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/duplex/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample2_Ivan_L2_D6/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/duplex/
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/l298l/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample3_Ivan_L1_D8/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/duplex/
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/l298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/l298l/duplex/variant_caller_outputs/
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/l298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/nol298l/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/nol298l/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/ABL/sample4_Ivan_L2_D8/sscs/variant_caller_outputs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample10_LTK_R1_Zot_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample10_LTK_R1_Zot_D6_A/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample10_LTK_R1_Zot_D6_A/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample11_LTK_R1_Zot_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample11_LTK_R1_Zot_D6_B/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample11_LTK_R1_Zot_D6_B/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample12_LTK_R2_D0/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample12_LTK_R2_D0/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample12_LTK_R2_D0/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample13_LTK_R2_ND_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample13_LTK_R2_ND_D6_A/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample13_LTK_R2_ND_D6_A/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample14_LTK_R2_ND_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample14_LTK_R2_ND_D6_B/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample15_LTK_R2_Lor_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample15_LTK_R2_Lor_D6_A/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample15_LTK_R2_Lor_D6_A/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample16_LTK_R2_Lor_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample16_LTK_R2_Lor_D6_B/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample16_LTK_R2_Lor_D6_B/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample17_LTK_R2_Zot_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample18_LTK_R2_Zot_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample5_LTK_R1_D0/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample5_LTK_R1_D0/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample5_LTK_R1_D0/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample6_LTK_R1_ND_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample6_LTK_R1_ND_D6_A/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample6_LTK_R1_ND_D6_A/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample7_LTK_R1_ND_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample7_LTK_R1_ND_D6_B/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample7_LTK_R1_ND_D6_B/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample8_LTK_R1_Lor_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample8_LTK_R1_Lor_D6_A/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample8_LTK_R1_Lor_D6_A/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample9_LTK_R1_Lor_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample9_LTK_R1_Lor_D6_B/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK/sample9_LTK_R1_Lor_D6_B/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample10_LTK_R1_Zot_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample10_LTK_R1_Zot_D6_A/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample10_LTK_R1_Zot_D6_A/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample11_LTK_R1_Zot_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample11_LTK_R1_Zot_D6_B/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample11_LTK_R1_Zot_D6_B/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample12_LTK_R2_D0/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample12_LTK_R2_D0/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample12_LTK_R2_D0/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample13_LTK_R2_ND_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample13_LTK_R2_ND_D6_A/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample13_LTK_R2_ND_D6_A/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample14_LTK_R2_ND_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample14_LTK_R2_ND_D6_B/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample15_LTK_R2_Lor_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample15_LTK_R2_Lor_D6_A/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample15_LTK_R2_Lor_D6_A/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample16_LTK_R2_Lor_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample16_LTK_R2_Lor_D6_B/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample16_LTK_R2_Lor_D6_B/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample17_LTK_R2_Zot_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample18_LTK_R2_Zot_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample5_LTK_R1_D0/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample5_LTK_R1_D0/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample5_LTK_R1_D0/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample6_LTK_R1_ND_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample6_LTK_R1_ND_D6_A/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample6_LTK_R1_ND_D6_A/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample7_LTK_R1_ND_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample7_LTK_R1_ND_D6_B/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample7_LTK_R1_ND_D6_B/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample8_LTK_R1_Lor_D6_A/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample8_LTK_R1_Lor_D6_A/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample8_LTK_R1_Lor_D6_A/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample9_LTK_R1_Lor_D6_B/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample9_LTK_R1_Lor_D6_B/duplex/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane29c/LTK_old/sample9_LTK_R1_Lor_D6_B/sscs/.DS_Store
    Ignored:    data/Consensus_Data/sscs_dcs_comparisons/
    Ignored:    data/Refs/.DS_Store
    Ignored:    data/region1234_spikein_growthrates_flowcytometry/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Ponatilink_Screens/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Ponatilink_Screens/backup_beforevariantcallerfix/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1234_Tileseq/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1234_Tileseq/data/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1234_Tileseq/output/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/Lane18_Comparisons_beforeintendedvsnonintendedstratification_12192024/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/Lane18_Comparisons_beforeintendedvsnonintendedstratification_12192024/cross-dose/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/Lane18_Comparisons_beforeintendedvsnonintendedstratification_12192024/cross-replicate/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/Lane18_Comparisons_beforeintendedvsnonintendedstratification_12192024/cross-species/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/Lane18_Comparisons_beforejumpyvariantcaller/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/Lane18_Comparisons_beforejumpyvariantcaller/cross-dose/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/Lane18_Comparisons_beforejumpyvariantcaller/cross-replicate/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/Lane18_Comparisons_beforejumpyvariantcaller/cross-species/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/cross-dose/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/cross-species/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/Attempt0_September2023_backup_ln28a/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/Attempt2_Feb2024_backup_ln192023included/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/Attempt3_3.17.24_backup_ln2728only/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/Attempt4_3.17.24_backup_ln2728only_countfiltered/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/Attempt5_12.19.24_beforeunintendedmutantsadded_/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/Attempt5_12.19.24_beforeunintendedmutantsadded_/baf3_r4_IL3_low_rep1vsrep2/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/Attempt5_12.19.24_beforeunintendedmutantsadded_/before_r4_filtering_3.24.24/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/backup_before_jumpydepths_fix_Jan2024/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/backup_before_mergesamplesfix/.DS_Store
    Ignored:    output/ABLEnrichmentScreens/ABL_Region234_Comparisons/sm_imatinib_plots/.DS_Store
    Ignored:    output/Twinstrand/ABL1AppOutput/.DS_Store
    Ignored:    shinyapp/.DS_Store

Untracked files:
    Untracked:  analysis/archive/ABL_cosmic_analysis.Rmd

Unstaged changes:
    Modified:   .DS_Store
    Modified:   analysis/.DS_Store
    Deleted:    analysis/ABL_cosmic_analysis.Rmd
    Modified:   analysis/Homepage_variant_interpretation.Rmd
    Modified:   output/ABLEnrichmentScreens/.DS_Store

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

---

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/ABL_region234_parser.Rmd) and HTML (docs/ABL_region234_parser.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	0a84364	haiderinam	2024-12-23	Updated ABL region 2,3,4 data parser
html	0a84364	haiderinam	2024-12-23	Updated ABL region 2,3,4 data parser

---

#Cleanup code for plotting
source("code/plotting/cleanup.R")
# source("code/compare_screens.R")
source("code/merge_samples.R")
source("code/plotting/heatmap_plotting_function.R")

# setwd("OneDrive - The PennsylABLfullkinase_allconditions_growthratesvania State University/RProjects/duplex_sequencing_screen/")

source("code/merge_samples.R")
getwd()

[1] "/Users/haiderinam/Library/CloudStorage/OneDrive-ThePennsylvaniaStateUniversity/RProjects/duplex_sequencing_screen"

source("code/res_residues_adder.R")

Section 1: Data Parsing.

compare_screens=function(before_screen1_identifier,
                         after_screen1_identifier,
                         before_screen2_identifier,
                         after_screen2_identifier,
                         cellcounts_matrix_location){

  # before_screen1_identifier=before_screen1_identifier
  # after_screen1_identifier=after_screen1_identifier
  # before_screen2_identifier=before_screen2_identifier
  # after_screen2_identifier=after_screen2_identifier
  # cellcounts_matrix_location=cellcounts_matrix_dir


  # Inputs: 1) Condition 1 baseline, 2) Condition 1 treated, 3) Condition 2 Baseline, 4) Condition 2 treated
  # 5)The location of the cell counts table
  # These inputs can have a single sample in the name or specify two samples to merge
  # This function takes in two screens and makes comparisons across them.
  # This function uses the compare samples function, that compares the before treatment and the treated timepoints of a screen
  # This function compares two screens
  # Inputs:
  # Which conditions would you like to compare:
  # before_screen1_identifier=comparisons$before_screen1_identifier[i]
  # after_screen1_identifier=comparisons$after_screen1_identifier[i]
  # before_screen2_identifier=comparisons$before_screen2_identifier[i]
  # after_screen2_identifier=comparisons$after_screen2_identifier[i]

  # before_screen1_identifier="KTRMD0"
  # before_screen1_identifier=c("KTRLD0","KTRLD0_FT")
  # after_screen1_identifier=c("KTRL1_D6","KTRL2_D6")
  # after_screen1_identifier="KTRM1_D6"
  # before_screen2_identifier="KTRMD0"
  # after_screen2_identifier=c("KTRM1_D6","KTRM2_D6")
  # after_screen2_identifier="KTRM2_D6"


  # before_screen1_identifier="BTR3ID0"
  # after_screen1_identifier="BTR3M_D6_A"
  # before_screen2_identifier="BTR3ID0"
  # after_screen2_identifier="BTR3M_D6_B"
  # cellcounts_matrix_location="data/Consensus_Data/novogene_lane23/TwistAllRegions_CellCounts_Matrix.csv"
  source("code/res_residues_adder.R")
  source("code/resmuts_adder.R")
  source("code/merge_samples.R")
  source("code/variants_parser.R")
  source("code/compare_samples.R")
  source("code/depth_finder.R")
  source("code/is_intended_adder.R")
  # after_screen1_counts=cell_counts_table%>%filter(Identifier%in%after_screen1_identifier)

  # The cell counts and the exact deltat is derived from a spreadsheet in the novogene lane 18 folder
  # cellcounts_matrix_location=cellcounts_matrix_dir
  cell_counts_table=read.csv(cellcounts_matrix_location)
  cell_counts_table=cell_counts_table%>%filter(!skip_flag%in%"TRUE")

  before_screen1_counts=cell_counts_table%>%filter(Identifier%in%before_screen1_identifier)
  after_screen1_counts=cell_counts_table%>%filter(Identifier%in%after_screen1_identifier)
  before_screen2_counts=cell_counts_table%>%filter(Identifier%in%before_screen2_identifier)
  after_screen2_counts=cell_counts_table%>%filter(Identifier%in%after_screen2_identifier)


  delta_t=mean(after_screen1_counts$Time_Hours)-mean(before_screen1_counts$Time_Hours) #hours
  cells_before=mean(before_screen1_counts$TotalCells) #total cells at before time point
  cells_after=mean(after_screen1_counts$TotalCells) #total cells at after time point
  netgr=mean(after_screen1_counts$Netgr_wodrug)


  # Running merge samples on all the directories specified for this sample
  # This if statements sees if there are two samples specified at a timepoint, and if so, merges those samples
  # Note that the code below can only do at max two separate sequencing samples. It can be modified in the future to allow multiple samples
  # if(length(before_screen1_counts[,1])>=2){
  #   before_timepoint=merge_samples(paste(before_screen1_counts$dirname_input[1],"/sscs",sep=""),paste(before_screen1_counts$dirname_input[2],"/sscs",sep=""))
  # } else {
  #   before_timepoint=read.csv(paste("data/Consensus_Data/",before_screen1_counts$dirname_input[1],"/sscs/variant_caller_outputs/variants_unique_ann.csv",sep=""))
  # }
  filepaths=paste(before_screen1_counts$dirname_input,"/sscs",sep="")
  before_timepoint=do.call(merge_samples,as.list(filepaths))

  before_timepoint=variants_parser(before_timepoint,cells_before)

  # Running merge samples on all the directories specified for this sample
  # This if statements sees if there are two samples specified at a timepoint, and if so, merges those samples
  # if(length(after_screen1_counts[,1])>=2){
  #   after_timepoint=merge_samples(paste(after_screen1_counts$dirname_input[1],"/sscs",sep=""),paste(after_screen1_counts$dirname_input[2],"/sscs",sep=""))
  # } else {
  #   after_timepoint=read.csv(paste("data/Consensus_Data/",after_screen1_counts$dirname_input[1],"/sscs/variant_caller_outputs/variants_unique_ann.csv",sep=""))
  # }
  filepaths=paste(after_screen1_counts$dirname_input,"/sscs",sep="")
  after_timepoint=do.call(merge_samples,as.list(filepaths))

  # after_timepoint=after_timepoint%>%mutate(ct=as.numeric(ct),ct=case_when(ct<=100~0.6,
  #                                                             T~ct))

  after_timepoint=variants_parser(after_timepoint,cells_after)

  ### Had do add in a piece of code to unlist these dataframes before running the compare samples code for some reason.
  before_timepoint <- as.data.frame(lapply(before_timepoint, unlist))
  after_timepoint <- as.data.frame(lapply(after_timepoint, unlist))
  ###
  # after_timepoint=after_timepoint

  before_after=compare_samples(before_timepoint,after_timepoint,netgr,delta_t)

  # before_after=before_after%>%filter(ct.x>=3)
  before_after_screen1=before_after


  ###### TSII Day 0 vs Day 4 #########





  delta_t=mean(after_screen2_counts$Time_Hours)-mean(before_screen2_counts$Time_Hours) #hours
  cells_before=mean(before_screen2_counts$TotalCells) #total cells at before time point
  cells_after=mean(after_screen2_counts$TotalCells) #total cells at after time point
  netgr=mean(after_screen2_counts$Netgr_wodrug)


  # Running merge samples on all the directories specified for this sample
  # This if statements sees if there are two samples specified at a timepoint, and if so, merges those samples
  # if(length(before_screen2_counts[,1])>=2){
  #   before_timepoint=merge_samples(paste(before_screen2_counts$dirname_input[1],"/sscs",sep=""),paste(before_screen2_counts$dirname_input[2],"/sscs",sep=""))
  # } else {
  #   before_timepoint=read.csv(paste("data/Consensus_Data/",before_screen2_counts$dirname_input[1],"/sscs/variant_caller_outputs/variants_unique_ann.csv",sep=""))
  # }
  filepaths=paste(before_screen2_counts$dirname_input,"/sscs",sep="")
  before_timepoint=do.call(merge_samples,as.list(filepaths))

  before_timepoint=variants_parser(before_timepoint,cells_before)

  # Running merge samples on all the directories specified for this sample
  # This if statements sees if there are two samples specified at a timepoint, and if so, merges those samples
  # if(length(after_screen2_counts[,1])>=2){
  #   after_timepoint=merge_samples(paste(after_screen2_counts$dirname_input[1],"/sscs",sep=""),paste(after_screen2_counts$dirname_input[2],"/sscs",sep=""))
  # } else {
  #   after_timepoint=read.csv(paste("data/Consensus_Data/",after_screen2_counts$dirname_input[1],"/sscs/variant_caller_outputs/variants_unique_ann.csv",sep=""))
  # }
  filepaths=paste(after_screen2_counts$dirname_input,"/sscs",sep="")
  after_timepoint=do.call(merge_samples,as.list(filepaths))
  
  # after_timepoint=after_timepoint%>%mutate(ct=as.numeric(ct),ct=case_when(ct<=100~0.6,
  #                                                             T~ct))

  after_timepoint=variants_parser(after_timepoint,cells_after)

  ### Had do add in a piece of code to unlist these dataframes before running the compare samples code for some reason.
  before_timepoint <- as.data.frame(lapply(before_timepoint, unlist))
  after_timepoint <- as.data.frame(lapply(after_timepoint, unlist))
  ###

  before_after=compare_samples(before_timepoint,after_timepoint,netgr,delta_t)

  # before_after=before_after%>%filter(ct.x>=3)
  before_after_screen2=before_after



  ############### Adding Count, Depth, and MAF columns for Ivan 2.20.23###########
  # a=before_after_screen1
  # b=before_after_screen2
  # before_after_screen1=a
  # before_after_screen2=b

  before_after_screen1=before_after_screen1%>%
    mutate(ct_screen1_before=ct.x,
           depth_screen1_before=depth.x,
           maf_screen1_before=maf.x,
           ct_screen1_after=ct.y,
           depth_screen1_after=depth.y,
           maf_screen1_after=maf.y)%>%
    dplyr::select(-c("ct.x","depth.x","maf.x","totalcells.x","totalmutant.x","ct.y","depth.y","maf.y","totalcells.y","totalmutant.y"))

  before_after_screen2=before_after_screen2%>%
    mutate(ct_screen2_before=ct.x,
           depth_screen2_before=depth.x,
           maf_screen2_before=maf.x,
           ct_screen2_after=ct.y,
           depth_screen2_after=depth.y,
           maf_screen2_after=maf.y)%>%
    dplyr::select(-c("ct.x","depth.x","maf.x","totalcells.x","totalmutant.x","ct.y","depth.y","maf.y","totalcells.y","totalmutant.y"))

  screen_compare=merge(before_after_screen1,
                       before_after_screen2,
                       by=c("ref_aa","protein_start","alt_aa","ref","alt","alt_start_pos","consequence_terms","ref_codon","alt_codon","alt_codon_shortest","n_nuc_min"),
                       all.x=T,
                       all.y=T,suffixes = c("_screen1","_screen2"))

  screen_compare=resmuts_adder(screen_compare)
  screen_compare=res_residues_adder(screen_compare)
  screen_compare=screen_compare%>%mutate(species=paste(ref_aa,protein_start,alt_aa,sep = ""))

  screen_compare_means=screen_compare%>%
    filter(!score_screen1%in%NA,!score_screen2%in%NA,!score_screen1%in%NaN,!score_screen2%in%NaN)%>%
    rowwise()%>%
    mutate(score_mean=mean(c(score_screen1,score_screen2)),
           netgr_obs_mean=mean(c(netgr_obs_screen1,netgr_obs_screen2)))

  # ###8/30/23 Change for Ivan (this update avoids remove NA counts on D0):
  screen_compare_means=screen_compare%>%
    # filter(!score_screen1%in%NA,!score_screen2%in%NA,!score_screen1%in%NaN,!score_screen2%in%NaN)%>%
    rowwise()%>%
    mutate(score_mean=mean(c(score_screen1,score_screen2)),
           netgr_obs_mean=mean(c(netgr_obs_screen1,netgr_obs_screen2)))
  ##### Adding whether an intended codon is a twist variant####
  screen_compare_means=is_intended_adder(screen_compare_means)

  # write.csv(screen_compare_means,"Imat_Enrichment_bgmerged_2.22.23.csv")
  ##############

  # before_after_screen1=before_after_screen1%>%
  #   mutate(ct_screen1=ct.x)%>%
  #   dplyr::select(-c("ct.x","depth.x","maf.x","totalcells.x","totalmutant.x","ct.y","depth.y","maf.y","totalcells.y","totalmutant.y"))
  #
  #
  # before_after_screen2=before_after_screen2%>%
  #   mutate(ct_screen2=ct.x)%>%
  #   dplyr::select(-c("ct.x","depth.x","maf.x","totalcells.x","totalmutant.x","ct.y","depth.y","maf.y","totalcells.y","totalmutant.y"))
  #
  # screen_compare=merge(before_after_screen1,
  #                      before_after_screen2,
  #                      by=c("ref_aa","protein_start","alt_aa","ref","alt","alt_start_pos","consequence_terms","ref_codon","alt_codon","alt_codon_shortest","n_nuc_min"),
  #                      all.x=T,
  #                      all.y=T)
  #
  # screen_compare=resmuts_adder(screen_compare)
  # screen_compare=screen_compare%>%mutate(species=paste(ref_aa,protein_start,alt_aa,sep = ""))
  screen_compare_means
}

# source("code/compare_screens.R")
# cellcounts_matrix_dir="data/Consensus_Data/novogene_lane23/TwistAllRegions_CellCounts_Matrix.csv"
cellcounts_matrix_dir="data/Consensus_Data/novogene_lane23/TwistAllRegions_CellCounts_Matrix_onlyln2728_attempt5.csv"

comparisons=read.csv("data/Consensus_Data/novogene_lane23/TwistAllRegions_Comparisons_Todo.csv")
comparisons=comparisons%>%filter(Completed%in%"FALSE")

for(i in 1:nrow(comparisons)){
# for(i in 1:1){
  # i=9
# for(i in 7:nrow(comparisons)){
# for(i in 1:8){
  # i=12
  # i=1
  dirname=comparisons$dirname[i]
  pathname=paste("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/",dirname,sep = "")
  # Create directory if it doesn't already exist
  if (!file.exists(pathname)){
    dir.create(pathname)
}
before_screen1_identifier=unlist(strsplit(comparisons$before_screen1_identifier[i],","))
after_screen1_identifier=unlist(strsplit(comparisons$after_screen1_identifier[i],","))
before_screen2_identifier=unlist(strsplit(comparisons$before_screen2_identifier[i],","))
after_screen2_identifier=unlist(strsplit(comparisons$after_screen2_identifier[i],","))

  # length(after_screen1_identifier)
# screen_compare_means=compare_screens(comparisons$before_screen1_identifier[i],
#                                      comparisons$after_screen1_identifier[i],
#                                      comparisons$before_screen2_identifier[i],
#                                      comparisons$after_screen2_identifier[i])
screen_compare_means=compare_screens(before_screen1_identifier,
                                     after_screen1_identifier,
                                     before_screen2_identifier,
                                     after_screen2_identifier,
                                     cellcounts_matrix_dir)

# Adding a flag,"depleted", for when a mutant completely drops out of a screen in both replicates
screen_compare_means=screen_compare_means%>%mutate(depleted=case_when(ct_screen1_after%in%0.5&&ct_screen2_after%in%0.5~"TRUE",
                                                                      T~"FALSE"))
###### Adding stringent count filters#### 3.17.24#####
# screen_compare_means=screen_compare_means%>%
#   mutate(ct_screen1_after=case_when(ct_screen1_after<=50~0.6,
#                                     T~ct_screen1_after),
#          ct_screen2_after=case_when(ct_screen2_after<=50~0.6,
#                                     T~ct_screen2_after))
#############################################

screen_compare_means_forexport=apply(screen_compare_means,2,as.character)
write.csv(screen_compare_means_forexport,file = paste("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/",dirname,"/screen_comparison_",dirname,".csv",sep=""))

# a=screen_compare_means%>% filter(is_intended%in%1)
# Plot 1. What does the heatmap look like from the average of the net growth rate?
start_site=comparisons$ABL_Start[i]
end_site=comparisons$ABL_End[i]
# source("code/plotting/heatmap_plotting_function.R")
heatmap_plotting_function(screen_compare_means%>%filter(is_intended%in%1),start_site,end_site,fill_variable = "netgr_obs_mean",fill_name = "Net growth rate")
ggsave(paste("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/",dirname,"/plot1_heatmap.pdf",sep=""),width=10,height=6,units="in",useDingbats=F)
# screen_compare_means2=screen_compare_means%>%filter(alt_codon%in%twist$Codon)

# Plot 2a: What do the correlations look like for net growth rate (show mutants in text)?
ggplot(screen_compare_means%>%filter(is_intended%in%1,protein_start%in%c(start_site:end_site)),aes(x=netgr_obs_screen1,y=netgr_obs_screen2,color=resmuts,label=species))+geom_text(size=2.5)+geom_abline()+cleanup+stat_cor(method = "pearson")+labs(color="Known\nResistant\nMutant")+scale_x_continuous("Net growth rate screen 1")+scale_y_continuous("Net growth rate screen 2")
ggsave(paste("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/",dirname,"/plot2a_Netgrowthrate_correlations_text.pdf",sep=""),width=6,height=4,units="in",useDingbats=F)

# Plot 2b: What do the correlations look like for enrichment scores (show mutants in points)?
ggplot(screen_compare_means%>%filter(is_intended%in%1,protein_start%in%c(start_site:end_site)),aes(x=netgr_obs_screen1,y=netgr_obs_screen2,label=species))+geom_point(color="black",shape=21,size=2,aes(fill=resmuts),alpha=.7)+geom_abline()+cleanup+stat_cor(method = "pearson")+labs(fill="Known\nResistant\nMutant")+scale_x_continuous("Net growth rate screen 1")+scale_y_continuous("Net growth rate screen 2")
ggsave(paste("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/",dirname,"/plot2b_Netgrowthrate_correlations_points.pdf",sep=""),width=6,height=4,units="in",useDingbats=F)
# Plot 2c: What do the correlations look like for enrichment scores (show mutants in text)?
ggplot(screen_compare_means%>%filter(is_intended%in%1,protein_start%in%c(start_site:end_site)),aes(x=score_screen1,y=score_screen2,color=resmuts,label=species))+geom_text(size=2.5)+geom_abline()+cleanup+ stat_cor(method = "pearson")+labs(color="Known\nResistant\nMutant")+scale_x_continuous("Enrichment score screen 1")+scale_y_continuous("Enrichment score screen 2")
ggsave(paste("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/",dirname,"/plot2c_Enrichmentscores_correlations_text.pdf",sep=""),width=6,height=4,units="in",useDingbats=F)

# Plot 2d: What do the correlations look like for net growth rates (show mutants in text + add depleted flag)?
ggplot(screen_compare_means%>%filter(is_intended%in%1,protein_start%in%c(start_site:end_site)),aes(x=netgr_obs_screen1,y=netgr_obs_screen2,label=species))+geom_point(color="black",shape=21,size=2,aes(fill=depleted),alpha=.7)+geom_abline()+cleanup+stat_cor(method = "pearson")+labs(fill="Depleting\nMutant")+scale_x_continuous("Net growth rate screen 1")+scale_y_continuous("Net growth rate screen 2")
ggsave(paste("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/",dirname,"/plot2d_Netgrowthrate_correlations_depletedmutants_points.pdf",sep=""),width=6,height=4,units="in",useDingbats=F)

# Plot 3a: Plots: what are the overall net growth rate distributions?
ggplot(screen_compare_means%>%filter(is_intended%in%1,protein_start%in%c(start_site:end_site)),aes(x=netgr_obs_mean,fill=resmuts))+geom_density(alpha=0.7)+cleanup+labs(fill="Known\nResistant\nMutant")+scale_x_continuous("Mean net growth rate of screens")
ggsave(paste("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/",dirname,"/plot3a_Netgrowthrate_distributions_resmuts.pdf",sep=""),width=6,height=4,units="in",useDingbats=F)
# Plot 3b: Plots: what are the net growth rate distributions?

library(reshape2)
screen_compare_melt=melt(screen_compare_means%>%filter(is_intended%in%1,protein_start%in%c(start_site:end_site))%>%dplyr::select(species,netgr_obs_screen1,netgr_obs_screen2),id.vars = "species",measure.vars =c("netgr_obs_screen1","netgr_obs_screen2"),variable.name = "Condition",value.name = "netgr_obs")


ggplot(screen_compare_melt,aes(x=netgr_obs,fill=Condition))+
  geom_density(alpha=0.7)+
  cleanup+
  scale_x_continuous("Net growth rate observed")+
  scale_fill_discrete(labels=c("Screen 1","Screen 2"))
ggsave(paste("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/",dirname,"/plot3b_Netgrowthrate_distributions.pdf",sep=""),width=6,height=4,units="in",useDingbats=F)

}

For Imatinib: Making a combined dataframe of all regions This chunk of code is the same as above except that the combined dataframes also include enrichment scores

This chunk of code also has median centering and normalizing the imatinib dataset by region. Region 2 and 3 scores and net growth rates were normalized by a constant factor of 0.7

This chunk of code also adds data for the F359C region by including data from a previous screen ########################################

# sum(r1$ct_screen1_before)
# sum(r2$ct_screen1_before)
# sum(r3$ct_screen1_before)
# sum(r4$ct_screen1_before)
############# IL3 SCREENS ############# 
# rm(list=ls())
r1=read.csv("output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/cross-replicate/baf3_IL3_rep1vsrep2_ft/screen_comparison_baf3_IL3_low_rep1vsrep2_ft.csv")

# Adding a dummy depleted variable. Ideally should add a case_when ct=0.5 clause to this region 1 dataset
r1$depleted=FALSE

r1=r1%>%filter(protein_start%in%c(240:321))

r2=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r2_IL3_low_rep1vsrep2/screen_comparison_baf3_r2_IL3_low_rep1vsrep2.csv")
r2=r2%>%filter(protein_start%in%c(322:393))

r3=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r3_IL3_low_rep1vsrep2/screen_comparison_baf3_r3_IL3_low_rep1vsrep2.csv")
r3=r3%>%filter(protein_start%in%c(394:465))

r4=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r4_IL3_low_rep1vsrep2/screen_comparison_baf3_r4_IL3_low_rep1vsrep2.csv")
r4=r4%>%filter(protein_start%in%c(466:518))


######### median centering r2 and 3 around 0.06
r2=r2%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
r3=r3%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
r4=r4%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)




il3_1_vsil3_2_all=rbind(r1,r2,r3,r4)

il3_1_vsil3_2_all=il3_1_vsil3_2_all%>%dplyr::select(-c("X",
                                         "alt_start_pos",
                                         "score_mean"))
                                        # "ct_screen1_before",
                                        #  "depth_screen1_before",
                                        #  "ct_screen1_after",
                                        #  "depth_screen1_after",
                                        #  "maf_screen1_before",
                                        #  "maf_screen1_after",
                                        #  "ct_screen2_before",
                                        #  "depth_screen2_before",
                                        #  "ct_screen2_after",
                                        #  "depth_screen2_after",
                                        #  "maf_screen2_before",
                                        #  "maf_screen2_after",
                                        #  "resmuts",
                                        #  "resresids",
                                        #  "netgr_obs_mean"

# il3_1_vsil3_2_all=il3_1_vsil3_2_all%>%rename(netgr.IL3.1=netgr_obs_screen1,netgr.IL3.2=netgr_obs_screen2,
#                                              score.IL3.1=score_screen1,score.IL3.2=score_screen2)
il3_1_vsil3_2_all=il3_1_vsil3_2_all%>%dplyr::select(c("species","consequence_terms"),"ref_aa",everything())


############# Imatinib low (300nM) screens  ############# 

r1=read.csv("output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/cross-replicate/baf3_Imat_low_rep1vsrep2_ft/screen_comparison_baf3_Imat_low_rep1vsrep2_ft.csv")
# Adding a dummy depleted variable. Ideally should add a case_when ct=0.5 clause to this region 1 dataset
r1$depleted=FALSE

r1=r1%>%filter(protein_start%in%c(240:321))



r2=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r2_Imat_low_rep1vsrep2/screen_comparison_baf3_r2_Imat_low_rep1vsrep2.csv")
r2=r2%>%filter(protein_start%in%c(322:393))

r3=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r3_Imat_low_rep1vsrep2/screen_comparison_baf3_r3_Imat_low_rep1vsrep2.csv")
r3=r3%>%filter(protein_start%in%c(394:465))

r4=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r4_Imat_low_rep1vsrep2/screen_comparison_baf3_r4_Imat_low_rep1vsrep2.csv")
r4=r4%>%filter(protein_start%in%c(466:518))

######### median centering r2 and 3 around 0.06
r2=r2%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
r3=r3%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
r4=r4%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
#########

imatlow_1_vsimatlow_2_all=rbind(r1,r2,r3,r4)

imatlow_1_vsimatlow_2_all=imatlow_1_vsimatlow_2_all%>%dplyr::select(-c("X",
                                         "alt_start_pos",
                                         "score_mean"))

# imatlow_1_vsimatlow_2_all=imatlow_1_vsimatlow_2_all%>%
#   rename(netgr.imat.low.1=netgr_obs_screen1,netgr.imat.low.2=netgr_obs_screen2,
#          score.imat.low.1=score_screen1,score.imat.low.2=score_screen2)
imatlow_1_vsimatlow_2_all=imatlow_1_vsimatlow_2_all%>%dplyr::select(c("species","consequence_terms"),"ref_aa",everything())



############# Imatinib medium 600nM SCREENS ############# 

r1=read.csv("output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/cross-replicate/baf3_Imat_medium_rep1vsrep2_ft/screen_comparison_baf3_Imat_medium_rep1vsrep2_ft.csv")
# Adding a dummy depleted variable. Ideally should add a case_when ct=0.5 clause to this region 1 dataset
r1$depleted=FALSE

r1=r1%>%filter(protein_start%in%c(240:321))

r2=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r2_Imat_medium_rep1vsrep2/screen_comparison_baf3_r2_Imat_medium_rep1vsrep2.csv")
r2=r2%>%filter(protein_start%in%c(322:393))

r3=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r3_Imat_medium_rep1vsrep2/screen_comparison_baf3_r3_Imat_medium_rep1vsrep2.csv")
r3=r3%>%filter(protein_start%in%c(394:465))

r4=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r4_Imat_medium_rep1vsrep2/screen_comparison_baf3_r4_Imat_medium_rep1vsrep2.csv")
r4=r4%>%filter(protein_start%in%c(466:518))

######### median centering r2 and 3 around 0.06
r2=r2%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
r3=r3%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
r4=r4%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
#########

imatmid_1_vsimatmid_2_all=rbind(r1,r2,r3,r4)

imatmid_1_vsimatmid_2_all=imatmid_1_vsimatmid_2_all%>%dplyr::select(-c("X",
                                         "alt_start_pos",
                                         "score_mean"))

# imatmid_1_vsimatmid_2_all=imatmid_1_vsimatmid_2_all%>%
#   rename(netgr.imat.mid.1=netgr_obs_screen1,netgr.imat.mid.2=netgr_obs_screen2,
#          score.imat.mid.1=score_screen1,score.imat.mid.2=score_screen2)
imatmid_1_vsimatmid_2_all=imatmid_1_vsimatmid_2_all%>%dplyr::select(c("species","consequence_terms"),"ref_aa",everything())


############# Imatinib high 1200nM SCREENS ############# 

r1=read.csv("output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/cross-replicate/baf3_Imat_high_rep1vsrep2_ft/screen_comparison_baf3_Imat_high_rep1vsrep2_ft.csv")
# Adding a dummy depleted variable. Ideally should add a case_when ct=0.5 clause to this region 1 dataset
r1$depleted=FALSE

r1=r1%>%filter(protein_start%in%c(240:321))

r2=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r2_Imat_high_rep1vsrep2/screen_comparison_baf3_r2_Imat_high_rep1vsrep2.csv")
r2=r2%>%filter(protein_start%in%c(322:393))

r3=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r3_Imat_high_rep1vsrep2/screen_comparison_baf3_r3_Imat_high_rep1vsrep2.csv")
r3=r3%>%filter(protein_start%in%c(394:465))

r4=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_r4_Imat_high_rep1vsrep2/screen_comparison_baf3_r4_Imat_high_rep1vsrep2.csv")
r4=r4%>%filter(protein_start%in%c(466:518))
######### median centering r2 and 3 around 0.06
r2=r2%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
r3=r3%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
r4=r4%>%mutate(netgr_obs_screen1=netgr_obs_screen1*.7,
               netgr_obs_screen2=netgr_obs_screen2*.7,
               score_screen1=score_screen1*.7,
               score_screen2=score_screen2*.7)
#########


imathigh_1_vsimathigh_2_all=rbind(r1,r2,r3,r4)

imathigh_1_vsimathigh_2_all=imathigh_1_vsimathigh_2_all%>%dplyr::select(-c("X",
                                         "alt_start_pos",
                                         "score_mean"))

# imathigh_1_vsimathigh_2_all=imathigh_1_vsimathigh_2_all%>%
#   rename(netgr.imat.high.1=netgr_obs_screen1,netgr.imat.high.2=netgr_obs_screen2,
#          score.imat.high.1=score_screen1,score.imat.high.2=score_screen2)
imathigh_1_vsimathigh_2_all=imathigh_1_vsimathigh_2_all%>%dplyr::select(c("species","consequence_terms"),"ref_aa",everything())

# colnames(pl1vs5_all)
il3_1_vsil3_2_all=il3_1_vsil3_2_all%>%dplyr::select(-"depleted")
imatlow_1_vsimatlow_2_all=imatlow_1_vsimatlow_2_all%>%dplyr::select(-"depleted")
imatmid_1_vsimatmid_2_all=imatmid_1_vsimatmid_2_all%>%dplyr::select(-"depleted")
imathigh_1_vsimathigh_2_all=imathigh_1_vsimathigh_2_all%>%dplyr::select(-"depleted")

# a= imatlow_1_vsimatlow_2_all %>%
  # filter(duplicated(species) & duplicated(species, fromLast = TRUE))

##############################Adding F359C data##########################
#######################IL3 Data################
tsi_il3=read.csv("output/ABLEnrichmentScreens/IL3_Enrichment_bgmerged_2.20.23.csv",header = T,stringsAsFactors = F)
tsi_il3=tsi_il3%>%filter(!((ct_screen2_after%in%0.5)&(ct_screen1_after%in%0.5)))
tsi_il3=tsi_il3%>%dplyr::select(-c("X",
                                   "alt_start_pos",
                                   "score_mean"))
tsi_il3=tsi_il3%>%dplyr::select(c("species","consequence_terms"),"ref_aa",everything())
tsi_il3=tsi_il3%>%mutate(netgr_obs_mean=mean(c(netgr_obs_screen1,netgr_obs_screen2)))
tsi_il3=is_intended_adder(tsi_il3)


il3_1_vsil3_2_all=il3_1_vsil3_2_all%>%filter(!protein_start%in%c(354:361))
il3_1_vsil3_2_all=rbind(il3_1_vsil3_2_all,
                         tsi_il3)
il3_1_vsil3_2_all=il3_1_vsil3_2_all%>%arrange(protein_start)
il3_1_vsil3_2_all$dose="il3"
il3_1_vsil3_2_all=il3_1_vsil3_2_all%>%dplyr::select("dose",everything())
il3_1_vsil3_2_all <- il3_1_vsil3_2_all %>%
  dplyr::select(-is_intended, everything()) %>%
  dplyr::relocate(is_intended, .after = n_nuc_min)
#######################Imatinib 300nM####################
tsi_imatinib=read.csv("output/ABLEnrichmentScreens/Imat_Enrichment_bgmerged_2.22.23.csv",header = T,stringsAsFactors = F)
tsi_imatinib=tsi_imatinib%>%filter(!((ct_screen2_after%in%0.5)&(ct_screen1_after%in%0.5)))
tsi_imatinib=tsi_imatinib%>%dplyr::select(-c("X",
                                   "alt_start_pos",
                                   "score_mean"))
tsi_imatinib=tsi_imatinib%>%dplyr::select(c("species","consequence_terms"),"ref_aa",everything())
tsi_imatinib=tsi_imatinib%>%mutate(netgr_obs_mean=mean(c(netgr_obs_screen1,netgr_obs_screen2)))
tsi_imatinib=is_intended_adder(tsi_imatinib)



imatlow_1_vsimatlow_2_all=imatlow_1_vsimatlow_2_all%>%filter(!protein_start%in%c(354:361))
imatlow_1_vsimatlow_2_all=rbind(imatlow_1_vsimatlow_2_all,
                         tsi_imatinib)
imatlow_1_vsimatlow_2_all=imatlow_1_vsimatlow_2_all%>%arrange(protein_start)
imatlow_1_vsimatlow_2_all$dose="300nM"
imatlow_1_vsimatlow_2_all=imatlow_1_vsimatlow_2_all%>%dplyr::select("dose",everything())
imatlow_1_vsimatlow_2_all <- imatlow_1_vsimatlow_2_all %>%
  dplyr::select(-is_intended, everything()) %>%
  dplyr::relocate(is_intended, .after = n_nuc_min)
#######################Imatinib 600nM####################
imatmid_1_vsimatmid_2_all=imatmid_1_vsimatmid_2_all%>%filter(!protein_start%in%c(354:361))
imatmid_1_vsimatmid_2_all=rbind(imatmid_1_vsimatmid_2_all,
                         tsi_imatinib)
imatmid_1_vsimatmid_2_all=imatmid_1_vsimatmid_2_all%>%arrange(protein_start)
imatmid_1_vsimatmid_2_all$dose="600nM"
imatmid_1_vsimatmid_2_all=imatmid_1_vsimatmid_2_all%>%dplyr::select("dose",everything())
imatmid_1_vsimatmid_2_all <- imatmid_1_vsimatmid_2_all %>%
  dplyr::select(-is_intended, everything()) %>%
  dplyr::relocate(is_intended, .after = n_nuc_min)
#######################Imatinib 1200nM####################
imathigh_1_vsimathigh_2_all=imathigh_1_vsimathigh_2_all%>%filter(!protein_start%in%c(354:361))
imathigh_1_vsimathigh_2_all=rbind(imathigh_1_vsimathigh_2_all,
                         tsi_imatinib)
imathigh_1_vsimathigh_2_all=imathigh_1_vsimathigh_2_all%>%arrange(protein_start)
imathigh_1_vsimathigh_2_all$dose="1200nM"
imathigh_1_vsimathigh_2_all=imathigh_1_vsimathigh_2_all%>%dplyr::select("dose",everything())
imathigh_1_vsimathigh_2_all <- imathigh_1_vsimathigh_2_all %>%
  dplyr::select(-is_intended, everything()) %>%
  dplyr::relocate(is_intended, .after = n_nuc_min)
############################################################


imatinib_all=rbind(il3_1_vsil3_2_all,
                   imatlow_1_vsimatlow_2_all,
                   imatmid_1_vsimatmid_2_all,
                   imathigh_1_vsimathigh_2_all)


write.csv(imatinib_all,"output/ABLEnrichmentScreens/ABL_Region234_Comparisons/ABLfullkinase_allconditions_growthrates_12.19.24.csv")

write.csv(il3_1_vsil3_2_all,"output/ABLEnrichmentScreens/ABL_Region234_Comparisons/il3_combined_counts_12.19.24.csv")

write.csv(imatlow_1_vsimatlow_2_all,"output/ABLEnrichmentScreens/ABL_Region234_Comparisons/imatinib_300nM_combined_counts_12.19.24.csv")

write.csv(imatmid_1_vsimatmid_2_all,"output/ABLEnrichmentScreens/ABL_Region234_Comparisons/imatinib_600nM_combined_counts_12.19.24.csv")

write.csv(imathigh_1_vsimathigh_2_all,"output/ABLEnrichmentScreens/ABL_Region234_Comparisons/imatinib_1200nM_combined_counts_12.19.24.csv")

Section 2: Plotting heatmaps.

imatinib_all=read.csv("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/ABLfullkinase_allconditions_growthrates_12.19.24.csv")[-1]
############### Plotting heatmaps with net growth rates#############
############### IL3 Net Gr############
source("code/plotting/heatmap_plotting_function.R")
heatmap_plotting_function(imatinib_all%>%filter(dose%in%"il3",!netgr_obs_screen2%in%"NaN"),240,512,fill_variable = "netgr_obs_mean",fill_name = "Net growth rate \n(Hrs^-1)")

Past versions of unnamed-chunk-6-1.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggsave("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_il3_heatmap.pdf",width=16,height=4,units="in",useDingbats=F)
############### IL3 Enrichment Score############
heatmap_plotting_function(imatinib_all%>%filter(dose%in%"il3",!score_screen2%in%"NaN"),240,512,fill_variable = "score_screen2",fill_name = "Enrichment Score")

Past versions of unnamed-chunk-6-2.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggsave("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_il3_heatmap_score.pdf",width=16,height=4,units="in",useDingbats=F)
############### Imat Low Net Gr############
heatmap_plotting_function(imatinib_all%>%filter(dose%in%"300nM",!netgr_obs_screen2%in%"NaN"),240,512,fill_variable = "netgr_obs_mean",fill_name = "Net growth rate \n(Hrs^-1)")

Past versions of unnamed-chunk-6-3.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggsave("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_imatinib_heatmap_300nM.pdf",width=16,height=4,units="in",useDingbats=F)
############## Imat Low Enrichment Score############
heatmap_plotting_function(imatinib_all%>%filter(dose%in%"300nM",!score_screen2%in%"NaN"),240,512,fill_variable = "score_screen2",fill_name = "Enrichment Score")

Past versions of unnamed-chunk-6-4.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggsave("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_imatinib_heatmap_300nM_score.pdf",width=16,height=4,units="in",useDingbats=F)
############### Imat Mid Net Gr############
heatmap_plotting_function(imatinib_all%>%filter(dose%in%"600nM",!netgr_obs_screen2%in%"NaN"),240,512,fill_variable = "netgr_obs_mean",fill_name = "Net growth rate \n(Hrs^-1)")

Past versions of unnamed-chunk-6-5.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggsave("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_imatinib_heatmap_600nM.pdf",width=16,height=4,units="in",useDingbats=F)
############### Imat Mid Enrichment Score############
heatmap_plotting_function(imatinib_all%>%filter(dose%in%"600nM",!score_screen2%in%"NaN"),240,512,fill_variable = "score_screen2",fill_name = "Enrichment Score")

Past versions of unnamed-chunk-6-6.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggsave("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_imatinib_heatmap_600nM_score.pdf",width=16,height=4,units="in",useDingbats=F)
############### Imat High Net Gr############
heatmap_plotting_function(imatinib_all%>%filter(dose%in%"1200nM",!netgr_obs_screen2%in%"NaN"),240,512,fill_variable = "netgr_obs_mean",fill_name = "Net growth rate \n(Hrs^-1)")

Past versions of unnamed-chunk-6-7.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggsave("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_imatinib_heatmap_1200nM.pdf",width=16,height=4,units="in",useDingbats=F)

############### Imat High Enrichment Score############
heatmap_plotting_function(imatinib_all%>%filter(dose%in%"1200nM",!score_screen2%in%"NaN"),240,512,fill_variable = "score_screen2",fill_name = "Enrichment Score")

Past versions of unnamed-chunk-6-8.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggsave("output/ABLEnrichmentScreens/ABL_Region234_Comparisons/baf3_imatinib_heatmap_1200nM_score_medianadjusted.pdf",width=16,height=4,units="in",useDingbats=F)

Section 3: Looking at replicate correlations in net growth rates.

I have new sequencing data from Lane 27b and Lane 28. Below, I am going to correlate the two datasets for region 4

codon_table=read.csv("data/codon_table.csv",header = T,stringsAsFactors = F)
twist_codons=codon_table%>%filter(Twist%in%T)
  # twist_alt_codon=twist_codons[twist_codons$Letter%in%alt_aa,"Codon"]
twist_alt_codon=twist_codons[,"Codon"]

For BTR4D0: I’ll look at the correlation between lane 28 sample 17 and lane 27b sample 9

# source("code/merge_samples.R")
# source("code/compare_samples.R")
# source("code/compare_samples_archive.R")

btr4d0a=read.csv("data/Consensus_Data/novogene_lane28c/sample17/sscs/variant_caller_outputs/variants_unique_ann.csv")
# btr4d0a=btr4d0a%>%filter(type%in%"mnv", protein_start%in%c(466:512))

btr4d0a=btr4d0a%>%filter(consequence_terms%in%"missense_variant",!ct%in%c(1,2,3))%>%mutate(maf=ct/depth)
btr4d0a=btr4d0a%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)
# btr4d0a=btr4d0a%>%filter(alt_codon%in%twist_alt_codon)
# btr4d0a=btr4d0a%>%mutate(twist=case_when(alt_codon%in%twist_alt_codon~T,
#                                          T~F))


btr4d0b=read.csv("data/Consensus_Data/novogene_lane27b/Sample9_10/sscs/variant_caller_outputs/variants_unique_ann.csv")
btr4d0b=btr4d0b%>%filter(consequence_terms%in%"missense_variant",!ct%in%c(1,2,3))%>%mutate(maf=ct/depth)
btr4d0b=btr4d0b%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)

btr4d0=merge(btr4d0a,btr4d0b,by = c("ref_aa","protein_start","alt_aa","type","alt_codon"))
btr4d0=btr4d0%>%filter(alt_codon%in%twist_alt_codon)
btr4d0=btr4d0%>%mutate(species=paste(ref_aa,protein_start,alt_aa,sep=""))
ggplot(btr4d0,
       aes(x=maf.x,y=maf.y,color=type))+geom_point()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  stat_cor(method = "pearson")

Past versions of unnamed-chunk-8-1.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggplot(btr4d0,
       aes(x=maf.x,y=maf.y,color=type,label=species))+
  geom_text()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  stat_cor(method = "pearson")

Past versions of unnamed-chunk-8-2.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

# btr4d0=btr4d0%>%filter(species%in%"Q491V")
btr4d0a=btr4d0a%>%filter(ref_aa%in%"Q",protein_start%in%491)
btr4d0b=btr4d0b%>%filter(ref_aa%in%"Q",protein_start%in%491)

Showing that there is a big difference between the twist and non-twist allele frequencies in SSCS libraries

btr4d0a=read.csv("data/Consensus_Data/novogene_lane28c/sample17/sscs/variant_caller_outputs/variants_unique_ann.csv")
# btr4d0a=btr4d0a%>%filter(type%in%"mnv", protein_start%in%c(466:512))

btr4d0a=btr4d0a%>%filter(consequence_terms%in%"missense_variant")%>%mutate(maf=ct/depth)
# btr4d0a=btr4d0a%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)
# btr4d0a=btr4d0a%>%filter(alt_codon%in%twist_alt_codon)
btr4d0a=btr4d0a%>%mutate(twist=case_when(alt_codon%in%twist_alt_codon~T,
                                         T~F))
ggplot(btr4d0a,aes(x=ct,fill=twist))+geom_density(alpha=.7)+scale_x_continuous(trans="log10")

Past versions of unnamed-chunk-9-1.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggplot(btr4d0a%>%filter(protein_start%in%c(465:512)),aes(x=ct,fill=twist))+geom_density(alpha=.7)+scale_x_continuous(trans="log10")

Past versions of unnamed-chunk-9-2.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

btr4d0b=read.csv("data/Consensus_Data/novogene_lane27b/sample9_10/sscs/variant_caller_outputs/variants_unique_ann.csv")
# btr4d0a=btr4d0a%>%filter(type%in%"mnv", protein_start%in%c(466:512))

btr4d0b=btr4d0b%>%filter(consequence_terms%in%"missense_variant")%>%mutate(maf=ct/depth)
# btr4d0a=btr4d0a%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)
# btr4d0a=btr4d0a%>%filter(alt_codon%in%twist_alt_codon)
btr4d0b=btr4d0b%>%mutate(twist=case_when(alt_codon%in%twist_alt_codon~T,
                                         T~F))
ggplot(btr4d0b,aes(x=ct,fill=twist))+geom_density(alpha=.7)+scale_x_continuous(trans="log10")

Past versions of unnamed-chunk-9-3.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggplot(btr4d0b%>%filter(protein_start%in%c(465:512)),aes(x=ct,fill=twist))+geom_density(alpha=.7)+scale_x_continuous(trans="log10")

Past versions of unnamed-chunk-9-4.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

btr4d0ab=merge(btr4d0a,btr4d0b,by=c("type",
                                    "alt_start_pos",
                                    "alt_end_pos",
                                    "ref",
                                    "ref_codon",
                                    "alt",
                                    "alt_codon",
                                    "frame_pos",
                                    "protein_start",
                                    "protein_end",
                                    "ref_aa",
                                    "alt_aa",
                                    "amino_acids",
                                    "consequence_terms",
                                    "twist"))

ggplot(btr4d0ab,aes(x=maf.x,y=maf.y,color=twist))+
  geom_point()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")

Past versions of unnamed-chunk-9-5.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

btr4d0ab=btr4d0ab%>%
  rowwise()%>%
  mutate(maf.mean=mean(maf.x,maf.y),
         maf.sd=sd(c(maf.x,maf.y)))

# btr4d0ab=btr4d0ab%>%
#   rowwise()%>%
#   mutate(maf.mean=mean(maf.x,maf.y),
#          maf.sd=sd(c(maf.x,maf.y)),
#          maf.zscore=(maf.mean-mean(btr4d0ab$maf.mean))/maf.sd)
sd(c(1,2))

[1] 0.7071068

ggplot(btr4d0ab,aes(x=maf.x,y=maf.y,color=log(maf.sd)))+
  geom_point()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  geom_abline()

Past versions of unnamed-chunk-9-6.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

For BTR4DMD6A vs B: I’ll look at the correlation between lane 28 sample 22 and lane 27b sample 11_12

# source("code/merge_samples.R")
# source("code/compare_samples.R")
# source("code/compare_samples_archive.R")

btr4d0a=read.csv("data/Consensus_Data/novogene_lane28c/sample22/sscs/variant_caller_outputs/variants_unique_ann.csv")
btr4d0a=btr4d0a%>%filter(consequence_terms%in%"missense_variant",!ct%in%c(1,2,3))%>%mutate(maf=ct/depth)
btr4d0a=btr4d0a%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)

btr4d0b=read.csv("data/Consensus_Data/novogene_lane27b/Sample11_12/sscs/variant_caller_outputs/variants_unique_ann.csv")
btr4d0b=btr4d0b%>%filter(consequence_terms%in%"missense_variant",!ct%in%c(1,2,3))%>%mutate(maf=ct/depth)
btr4d0b=btr4d0b%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)

btr4d0=merge(btr4d0a,btr4d0b,by = c("ref_aa","protein_start","alt_aa","type","alt_codon"))
btr4d0b=btr4d0b%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)
# x=btr4d0%>%filter(protein_start%in%"486")
btr4d0=merge(btr4d0a,btr4d0b,by = c("ref_aa","protein_start","alt_aa","type","alt_codon"))
btr4d0=btr4d0%>%filter(alt_codon%in%twist_alt_codon)
btr4d0=btr4d0%>%mutate(species=paste(ref_aa,protein_start,alt_aa,sep=""))

ggplot(btr4d0,
       aes(x=maf.x,y=maf.y,color=type))+geom_point()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  stat_cor(method = "pearson")

Past versions of unnamed-chunk-10-1.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggplot(btr4d0,
       aes(x=maf.x,y=maf.y,color=type,label=species))+
  geom_text()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  stat_cor(method = "pearson")

Past versions of unnamed-chunk-10-2.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

For BTR4DHD6A vs B: I’ll look at the correlation between lane 28 sample 23 and 24 Interestingly, the selection replicate correlation is HIGHER than the library prep replicate correlation. i.e. the noise from one library prep date to another library prep date seems higher than the noise from independent selection replicates as long as they were prepped on the same day. For instance, Lane 27b sample 9_10 vs Lane 28 sample 17 (R4D0) has a lower correlation than Lane 28c sample 23 vs sample 24 (R4IHD6 A vs R4IHD6 B)

# source("code/merge_samples.R")
# source("code/compare_samples.R")
# source("code/compare_samples_archive.R")

btr4d0a=read.csv("data/Consensus_Data/novogene_lane28c/sample23/sscs/variant_caller_outputs/variants_unique_ann.csv")
btr4d0a=btr4d0a%>%filter(consequence_terms%in%"missense_variant",!ct%in%c(1,2,3))%>%mutate(maf=ct/depth)
btr4d0a=btr4d0a%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)

btr4d0b=read.csv("data/Consensus_Data/novogene_lane28c/sample24/sscs/variant_caller_outputs/variants_unique_ann.csv")
btr4d0b=btr4d0b%>%filter(consequence_terms%in%"missense_variant",!ct%in%c(1,2,3))%>%mutate(maf=ct/depth)
btr4d0b=btr4d0b%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)

btr4d0=merge(btr4d0a,btr4d0b,by = c("ref_aa","protein_start","alt_aa","type","alt_codon"))
btr4d0=btr4d0%>%filter(alt_codon%in%twist_alt_codon)
btr4d0=btr4d0%>%mutate(species=paste(ref_aa,protein_start,alt_aa,sep=""))

ggplot(btr4d0,
       aes(x=maf.x,y=maf.y,color=type))+geom_point()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  stat_cor(method = "pearson")

Past versions of unnamed-chunk-11-1.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggplot(btr4d0,
       aes(x=maf.x,y=maf.y,color=type,label=species))+
  geom_text()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  stat_cor(method = "pearson")

Past versions of unnamed-chunk-11-2.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

For BTR4DID6A vs B: I’ll look at the correlation between lane 28 sample 18 and 19

# source("code/merge_samples.R")
# source("code/compare_samples.R")
# source("code/compare_samples_archive.R")

btr4d0a=read.csv("data/Consensus_Data/novogene_lane28c/sample18/sscs/variant_caller_outputs/variants_unique_ann.csv")
btr4d0a=btr4d0a%>%filter(consequence_terms%in%"missense_variant",!ct%in%c(1,2,3,4,5,6))%>%mutate(maf=ct/depth)
btr4d0a=btr4d0a%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)

btr4d0b=read.csv("data/Consensus_Data/novogene_lane28c/sample19/sscs/variant_caller_outputs/variants_unique_ann.csv")
btr4d0b=btr4d0b%>%filter(consequence_terms%in%"missense_variant",!ct%in%c(1,2,3,4,5,6))%>%mutate(maf=ct/depth)
btr4d0b=btr4d0b%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)

btr4d0=merge(btr4d0a,btr4d0b,by = c("ref_aa","protein_start","alt_aa","type","alt_codon"))
# btr4d0=btr4d0%>%filter(!alt_codon%in%twist_alt_codon)
btr4d0=btr4d0%>%filter(alt_codon%in%twist_alt_codon)
btr4d0=btr4d0%>%mutate(species=paste(ref_aa,protein_start,alt_aa,sep=""))

ggplot(btr4d0,
       aes(x=maf.x,y=maf.y,color=type))+geom_point()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  stat_cor(method = "pearson")

Past versions of unnamed-chunk-12-1.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggplot(btr4d0,
       aes(x=maf.x,y=maf.y,color=type,label=species))+
  geom_text()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  stat_cor(method = "pearson")

Past versions of unnamed-chunk-12-2.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

# Checking for duplicates in all the data

a= r1 %>%
  filter(duplicated(species) & duplicated(species, fromLast = TRUE))

a= r2 %>%
  filter(duplicated(species) & duplicated(species, fromLast = TRUE))

a= r4 %>%
  filter(duplicated(species) & duplicated(species, fromLast = TRUE))

a= imatinib_all %>%
  filter(duplicated(species) & duplicated(species, fromLast = TRUE))

# a=imathigh_1_vsimathigh_2_all%>%filter(protein_start%in%c(394:465))


analysis=il3_1_vsil3_2_all%>%mutate(region=case_when(protein_start%in%c(240:321)~"region1",
                                                     protein_start%in%c(322:393)~"region2",
                                                     protein_start%in%c(394:465)~"region3",
                                                     protein_start%in%c(465:518)~"region4",
                                                     T~"noregion"))
analysis_sum=analysis%>%group_by(region,alt_aa)%>%summarise(netgr.IL3.1=mean(netgr.IL3.1,na.rm = T),
                                                        netgr.IL3.2=mean(netgr.IL3.2,na.rm = T))

ggplot(analysis_sum,aes(x=alt_aa,y=netgr.IL3.1))+geom_point()+facet_wrap(~region)
# a=il3_1_vsil3_2_all%>%f

a= imathigh_1_vsimathigh_2_all %>%
  filter(protein_start%in%"459")

For BTR2LD0A vs B: I’ll look at the correlation between lane 28 sample 23 and 24

# source("code/merge_samples.R")
# source("code/compare_samples.R")
# source("code/compare_samples_archive.R")

btr4d0a=read.csv("data/Consensus_Data/novogene_lane28c_old/sample6/sscs/variant_caller_outputs/variants_unique_ann.csv")
btr4d0a=btr4d0a%>%filter(consequence_terms%in%"missense_variant",!ct%in%c(1,2,3))%>%mutate(maf=ct/depth)
btr4d0a=btr4d0a%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)

btr4d0b=read.csv("data/Consensus_Data/novogene_lane28c/sample6/sscs/variant_caller_outputs/variants_unique_ann.csv")
btr4d0b=btr4d0b%>%filter(consequence_terms%in%"missense_variant",!ct%in%c(1,2,3))%>%mutate(maf=ct/depth)
btr4d0b=btr4d0b%>%dplyr::select(ref_aa,protein_start,alt_aa,type,maf,alt_codon)

btr4d0=merge(btr4d0a,btr4d0b,by = c("ref_aa","protein_start","alt_aa","type","alt_codon"))
btr4d0=btr4d0%>%filter(alt_codon%in%twist_alt_codon)
btr4d0=btr4d0%>%mutate(species=paste(ref_aa,protein_start,alt_aa,sep=""))

ggplot(btr4d0,
       aes(x=maf.x,y=maf.y,color=type))+geom_point()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  stat_cor(method = "pearson")

Past versions of unnamed-chunk-14-1.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

ggplot(btr4d0,
       aes(x=maf.x,y=maf.y,color=type,label=species))+
  geom_text()+
  scale_x_continuous(trans="log10")+
  scale_y_continuous(trans="log10")+
  stat_cor(method = "pearson")

Past versions of unnamed-chunk-14-2.png

Version	Author	Date
0a84364	haiderinam	2024-12-23

Session information

sessionInfo()

R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS  10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] pROC_1.16.2        ggpubr_0.4.0       RColorBrewer_1.1-2 doParallel_1.0.15 
 [5] iterators_1.0.12   foreach_1.5.0      tictoc_1.0         plotly_4.9.2.1    
 [9] ggplot2_3.3.3      dplyr_1.0.6        stringr_1.4.0     

loaded via a namespace (and not attached):
 [1] httr_1.4.2        sass_0.4.1        tidyr_1.1.3       jsonlite_1.7.2   
 [5] viridisLite_0.3.0 carData_3.0-3     bslib_0.3.1       assertthat_0.2.1 
 [9] cellranger_1.1.0  yaml_2.2.1        pillar_1.6.1      backports_1.1.7  
[13] glue_1.4.1        digest_0.6.25     promises_1.1.0    ggsignif_0.6.0   
[17] colorspace_1.4-1  htmltools_0.5.2   httpuv_1.5.2      plyr_1.8.6       
[21] pkgconfig_2.0.3   broom_0.7.6       haven_2.4.1       purrr_0.3.4      
[25] scales_1.1.1      whisker_0.4       openxlsx_4.1.5    later_1.0.0      
[29] rio_0.5.16        git2r_0.27.1      tibble_3.1.2      generics_0.0.2   
[33] farver_2.0.3      car_3.0-7         ellipsis_0.3.2    withr_2.4.2      
[37] lazyeval_0.2.2    magrittr_2.0.1    crayon_1.4.1      readxl_1.3.1     
[41] evaluate_0.14     fs_1.4.1          fansi_0.4.1       rstatix_0.6.0    
[45] forcats_0.5.1     foreign_0.8-78    tools_4.0.0       data.table_1.14.8
[49] hms_1.1.0         lifecycle_1.0.0   munsell_0.5.0     zip_2.0.4        
[53] compiler_4.0.0    jquerylib_0.1.4   rlang_0.4.11      grid_4.0.0       
[57] htmlwidgets_1.5.1 labeling_0.3      rmarkdown_2.14    gtable_0.3.0     
[61] codetools_0.2-16  abind_1.4-5       DBI_1.1.0         curl_4.3         
[65] R6_2.4.1          knitr_1.28        fastmap_1.1.0     utf8_1.1.4       
[69] workflowr_1.6.2   rprojroot_1.3-2   stringi_1.7.5     Rcpp_1.0.4.6     
[73] vctrs_0.3.8       tidyselect_1.1.0  xfun_0.31