Home

workflowr

• Summary
• Checks
• Past versions

Last updated: 2023-09-02

Checks: 1 1

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: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Repository version: 57fd1e7

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 57fd1e7. 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:    data/Consensus_Data/.Rhistory
    Ignored:    data/Consensus_Data/Novogene_lane11/.DS_Store
    Ignored:    data/Consensus_Data/Novogene_lane11/sample1/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample1/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample1/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample1/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample1/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample1/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample2/archive/sscs_aligned_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample2/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample2/duplex/variant_caller_outputs/archive_ensembl/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample2/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample2/sscs/variant_caller_outputs/archive_ensembl/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample2/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample3/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample3/duplex/variant_caller_outputs/archive_ensembl/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample3/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample3/sscs/variant_caller_outputs/archive ensembl/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample3/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample4/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample4/duplex/variant_caller_outputs/archive ensembl/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample4/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample4/sscs/variant_caller_outputs/archive ensembl/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample4/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample5/variant_caller_outputs/sscs_L858R_aligned_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample5/variant_caller_outputs/sscs_L858R_aligned_filtered_sample5.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample6/archive/sscs_aligned_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample6/sscs_L858R_aligned_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample6/variant_caller_outputs/variants_ann_sample6.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample7/sscs/variant_caller_outputs/archive ensembl/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane11/sample7/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample1/low_sscscounts/sscs_aligned_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample1/low_sscscounts/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample1/sscs_aligned_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample1/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample3/sscs_combined_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample3/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample5/sscs_combined_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample5/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample7/sscs_combined_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample7/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample9/sscs_combined_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane12/sample9/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample1/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample1/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample1/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample1/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample10/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample10/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample10/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample10/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample10/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample11/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample11/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample11/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample11/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample11/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample12/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample12/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample12/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample12/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample12/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample12/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample2/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample2/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample3/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample3/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample4/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample4/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample5/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample5/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample6/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample6/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample7/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample7/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample7/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample7/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample7/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample8/
    Ignored:    data/Consensus_Data/Novogene_lane13/sample9/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample9/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample9/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample9/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane13/sample9/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample10_combined/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample10_combined/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample10_combined/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample10_combined/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample10_combined/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample10_combined/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample11/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample11/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample11/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample11/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample11/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample12/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample12/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample12/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample12/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample12/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample12/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample13/
    Ignored:    data/Consensus_Data/Novogene_lane14/sample14_combined/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample14_combined/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample14_combined/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample14_combined/sscs.filt_1.fa.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample14_combined/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample14_combined/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample14_combined/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample14b/
    Ignored:    data/Consensus_Data/Novogene_lane14/sample15/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample15/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample15/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample15/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample15/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample15/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample16/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample16/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample16/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample16/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample16/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample16/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample17/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample17/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample17/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample17/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample17/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample17/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample18/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample18/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample18/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample18/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample18/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample18/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample1_combined/
    Ignored:    data/Consensus_Data/Novogene_lane14/sample2_combined/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample2_combined/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample3/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample3/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample4/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample4/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample5/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample5/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample6/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample6/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample7/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample7/variant_caller_outputs/duplex/
    Ignored:    data/Consensus_Data/Novogene_lane14/sample7/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample8/
    Ignored:    data/Consensus_Data/Novogene_lane14/sample9/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample9/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample9/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample9/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/Novogene_lane14/sample9/sscs/variant_caller_outputs/variants_ann.csv.gz
    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/Ranomics_Pooled/
    Ignored:    data/Consensus_Data/archive/
    Ignored:    data/Consensus_Data/novogene_lane15/sample_1/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_1/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_1/firstrun(lowsequencing)/
    Ignored:    data/Consensus_Data/novogene_lane15/sample_1/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_2/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_2/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_2/firstrun(lowsequencing)/sscs/
    Ignored:    data/Consensus_Data/novogene_lane15/sample_2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_2/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/firstrun(lowsequencing)/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/ngs/Sample3_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/ngs/sample3a(firsthalf)/Sample3_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/ngs/sample3a(firsthalf)/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/ngs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_3/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/firstrun(lowsequencing)/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/firstrun(lowsequencing)/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_4/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/firstrun(lowsequencing)/duplex/variant_caller_outputs/variants_ann.csv.gz
    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/firstrun(lowsequencing)/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_5/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/firstrun(lowsequencing)/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/firstrun(lowsequencing)/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_6/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/duplex/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/firstrun(lowsequencing)/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/firstrun(lowsequencing)/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/firstrun(lowsequencing)/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/firstrun(lowsequencing)/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/sscs/variant_caller_outputs/archive/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane15/sample_7/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample10/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample10/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample10/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample11/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample11/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample11/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample12/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample12/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample12/sscs/
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample13/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample13/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample13/sscs/
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample14/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample14/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample14/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample14/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample1_combined/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample1_combined/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample1_combined/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample1_combined/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample2/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample2/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample2/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample3/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample3/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample3/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample4/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample4/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample4/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample5/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample5/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample5/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample6/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample6/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample6/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample7/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample7/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample7/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample8/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample8/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample8/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample9/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample9/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/Sample9/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16a/duplex/
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample10/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample10/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample10/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample11/
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample15/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample15/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample15/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample15/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample1_combined/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample1_combined/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample1_combined/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample1_combined/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample2/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample2/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample2/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample3/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample3/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample3/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample4/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample4/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample4/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample5/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample5/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample5/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample6/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample6/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample6/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample7_combined/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample7_combined/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample7_combined/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample7_combined/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample8_combined/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample8_combined/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/variant_caller_outputs/archive/
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample8_combined/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample9/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample9/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane16b/Sample9/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample10/duplex/
    Ignored:    data/Consensus_Data/novogene_lane17/sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample10/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample11/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample11/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample11/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/duplex/low_depth/
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/low_depth/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample1_combined/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample2/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample2/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample2/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample3/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample3/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample3/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample4/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample4/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample4/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/low_seq_depth/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/low_seq_depth/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/low_seq_depth/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/low_seq_depth/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample5/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample6/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample6/low_seq_depths/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample6/low_seq_depths/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample6/low_seq_depths/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample6/low_seq_depths/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample6/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/low_seq_depths/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/low_seq_depths/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/low_seq_depths/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/low_seq_depths/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample7/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample8/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample8/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample9/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample9/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17/sample9/sscs/variant_caller_outputs/variants_ann.csv.gz
    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/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample1/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample1/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample1/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample2/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample2/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane17b/Sample2/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample1/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    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/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/ngs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/ngs/Sample_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/ngs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample10/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/l298l/sscs/variant_caller_outputs/slow_variantcaller_outputs_forcomparison/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/ngs/Sample_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/ngs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample11/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample12/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample12/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample12/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample12/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample12/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample12/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample12/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample12/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/ngs/Sample_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/ngs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample13/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/l298l/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/ngs/Sample_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/ngs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/nol298l/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample14/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample15/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample16/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample17/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample17/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample17/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample17/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample17/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample17/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample17/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample17/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample18/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/l298l/sscs/variant_caller_outputs/fastercaller/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample2/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    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/l298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/nol298l/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample3/sscs/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/ngs/Sample_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/ngs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample4/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/ngs/Sample_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/ngs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample5/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample6/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample7/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample7/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample7/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample7/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample7/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample7/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample7/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample7/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample8/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample8/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample8/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample8/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample8/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample8/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample8/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample8/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/l298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/l298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/nol298l/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/nol298l/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/sample9/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/l298l/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/nol298l/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample3/sscs/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/l298l/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/nol298l/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample5/sscs/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/l298l/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/l298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/l298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/nol298l/duplex/
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/nol298l/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/nol298l/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane18/tlane18a_sample6/sscs/
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample1/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample1/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample1/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample1/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample10/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample10/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample10/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample11/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample11/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample11/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample12/duplex/
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample12/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample12/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample2/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample2/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample2/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample3/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample3/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample3/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample4/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample4/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample4/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample5/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample5/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample5/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample6/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample6/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample6/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample7/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample7/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample7/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample8/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample8/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample8/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample9/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample9/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19a_Sample9/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample1/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample1/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample1/sscs/
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample10/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample10/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample10/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample11/duplex/
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample11/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample12/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample12/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample12/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample12/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample13/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample13/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample13/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample13/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample14/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample14/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample14/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample14/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample15/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample15/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample15/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample15/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample16/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample16/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample16/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample16/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample2/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample2/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample2/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample3/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample3/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample3/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample4/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample4/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample4/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample5/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample5/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample5/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample6/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample6/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample6/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample7/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample7/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample7/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample8/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample8/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample8/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample9/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample9/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19/Ln19b_Sample9/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample10/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample10/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample10/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample10/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample11/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample11/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample11/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample11/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample2/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample2/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample2/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample3/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample3/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample3/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample4/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample4/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample4/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample5/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample5/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample5/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample6/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample6/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample6/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample7/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample7/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample7/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample7/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample8/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample8/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample8/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample8/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample9/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample9/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19a_Sample9/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19b_Sample9/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19b_Sample9/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19b_Sample9/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane19_20/Ln19b_Sample9/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample1/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample1/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample1/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample1/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample2/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample2/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample2/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample2/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample3/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample3/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample3/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample3/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample4/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample4/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample4/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample4/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample5/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample5/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample5/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample5/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample6/duplex/
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample6/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample6/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample7/
    Ignored:    data/Consensus_Data/novogene_lane22/Lane22_Sample8/
    Ignored:    data/Consensus_Data/novogene_lane23/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample13/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample13/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample13/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample13/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample13/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample14/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample14/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample14/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample14/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample14/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample15/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample15/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample15/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample15/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample15/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample16/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample16/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample16/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample16/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample16/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample17/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample17/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample17/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample17/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample17/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample18/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample18/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample18/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample18/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample18/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample19/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample19/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample19/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample19/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample19/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample20/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample20/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample20/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample20/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample20/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample21/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample21/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample21/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample21/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample21/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample22/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample22/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample22/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample22/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample22/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample23/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample23/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample23/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample23/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample23/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample24/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample24/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample24/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample24/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample24/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample25/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample25/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample25/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample25/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample25/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample26/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample26/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample26/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample26/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample26/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample27/.DS_Store
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample27/duplex/duplex_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample27/duplex/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample27/sscs/sscs_sorted_filtered.tsv.gz
    Ignored:    data/Consensus_Data/novogene_lane23/Lane23_Sample27/sscs/variant_caller_outputs/variants_ann.csv.gz
    Ignored:    data/Consensus_Data/sscs_dcs_comparisons/
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/NA/
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/baf3_IL3_low_rep1vsrep2/
    Ignored:    output/ABLEnrichmentScreens/ABL_Region1_Lane18_Comparisons/baf3_Imat_Lowvsk562_Imat_Medium/
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/il3_indep_1.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/il3_indep_1.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/il3_indep_2.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/il3_indep_2.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/il3_indep_3.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/il3_indep_3.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/sorted_1.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/sorted_1.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/sorted_2.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/sorted_2.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/sorted_3.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane3/sorted_3.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/il3_indep_1.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/il3_indep_1.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/il3_indep_2.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/il3_indep_2.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/il3_indep_3.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/il3_indep_3.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/il3_indep_4.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/il3_indep_4.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/il3_indep_5.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/il3_indep_5.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_1.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_1.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_2.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_2.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_3.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_3.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_4.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_4.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_5.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_5.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_6.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane4/sorted_6.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_High_D2.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_High_D2.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_High_D4.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_High_D4.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_Low_D2.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_Low_D2.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_Low_D4.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_Low_D4.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_Medium_D2.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_Medium_D2.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_Medium_D4.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP4_Im_Medium_D4.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_High_D2.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_High_D2.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_High_D4.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_High_D4.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_Low_D2.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_Low_D2.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_Low_D4.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_Low_D4.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_Medium_D2.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_Medium_D2.1.consensus.variant-calls.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_Medium_D4.1.consensus.variant-calls.genome.vcf.gz
    Ignored:    output/Twinstrand/ABL1AppOutput/Novogene_Lane5/RP5_Im_Medium_D4.1.consensus.variant-calls.vcf.gz

Untracked files:
    Untracked:  data/Consensus_Data/novogene_lane23/TwistAllRegions_CellCounts_Matrix.csv
    Untracked:  data/Consensus_Data/novogene_lane23/TwistAllRegions_Comparisons_Todo.csv

Unstaged changes:
    Modified:   .DS_Store
    Modified:   analysis/index.Rmd
    Modified:   data/.DS_Store
    Modified:   data/Consensus_Data/.DS_Store
    Modified:   output/.DS_Store
    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/index.Rmd) and HTML (docs/index.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	57fd1e7	haiderinam	2023-08-30	Updated various analyses and added to website
html	57fd1e7	haiderinam	2023-08-30	Updated various analyses and added to website
html	f9eea37	haiderinam	2023-08-30	2023 Updates
Rmd	8202ef7	haiderinam	2023-04-10	Added BE vs SM analyses on putative mutant
html	8202ef7	haiderinam	2023-04-10	Added BE vs SM analyses on putative mutant
Rmd	60b906b	haiderinam	2023-04-10	Added ROC analyses on BE-SM data
html	60b906b	haiderinam	2023-04-10	Added ROC analyses on BE-SM data
Rmd	a33eea5	haiderinam	2023-03-25	Added ABL CDF Analyses of evenness
html	a33eea5	haiderinam	2023-03-25	Added ABL CDF Analyses of evenness
Rmd	81a5af3	haiderinam	2023-02-25	Added shortest codon finder function
Rmd	fa7baf1	haiderinam	2022-12-15	Updates to the variant caller
html	fabfb30	haiderinam	2022-12-09	Build site.
Rmd	077edd0	haiderinam	2022-12-09	Added K562 Webpage
html	077edd0	haiderinam	2022-12-09	Added K562 Webpage
Rmd	cec2e31	haiderinam	2022-12-08	Added error rate analyses
html	cec2e31	haiderinam	2022-12-08	Added error rate analyses
html	404fc72	haiderinam	2022-11-04	Build site.
Rmd	ff4b4e8	haiderinam	2022-11-04	wflow_publish("analysis/index.Rmd")
Rmd	3a2f887	haiderinam	2022-11-04	Added analyses of IL3 independence
Rmd	6f54acf	haiderinam	2022-11-04	Added analyses of SSCS vs DCS error rates
html	28519e7	haiderinam	2022-10-29	Build site.
Rmd	ba25cb7	haiderinam	2022-10-29	wflow_publish("analysis/index.Rmd")
Rmd	7ed0af8	haiderinam	2022-08-22	August 2022 Updates
html	86ce8ca	haiderinam	2022-08-22	August 2022 Update
html	f368371	haiderinam	2020-08-13	Build site.
html	7fe0f9b	haiderinam	2020-07-06	Build site.
Rmd	e4a901d	haiderinam	2020-07-06	wflow_publish("analysis/index.Rmd")
html	231d21d	haiderinam	2020-06-07	Build site.
html	8f50f99	haiderinam	2020-06-07	Build site.
Rmd	5da3af0	haiderinam	2020-06-07	wflow_publish("analysis/index.Rmd")
html	75ddcb1	haiderinam	2020-06-02	Build site.
Rmd	a173683	haiderinam	2020-06-02	wflow_publish("analysis/index.Rmd")
html	bd2dec5	haiderinam	2020-06-02	Build site.
Rmd	1bb5940	haiderinam	2020-06-02	wflow_publish("analysis/index.Rmd")
html	c43acef	haiderinam	2020-06-02	Build site.
Rmd	d5c9f64	haiderinam	2020-06-02	wflow_publish("analysis/index.Rmd")
html	eaca616	haiderinam	2020-04-20	Build site.
Rmd	2bba93e	haiderinam	2020-04-20	wflow_publish("analysis/*.Rmd")
html	05e3df6	haiderinam	2020-04-07	Build site.
html	1c86f69	haiderinam	2020-04-07	Build site.
Rmd	e731909	haiderinam	2020-04-07	wflow_publish("analysis/index.Rmd")
html	4516a7f	haiderinam	2020-04-06	Build site.
Rmd	3a57291	haiderinam	2020-04-06	wflow_publish(files = "analysis/index.Rmd")
html	c2930d5	haiderinam	2020-04-03	Build site.
Rmd	52f6884	haiderinam	2020-04-03	wflow_publish("analysis/*.Rmd")
html	6af2cdc	haiderinam	2020-04-03	Build site.
Rmd	5cda9d3	haiderinam	2020-04-03	wflow_publish("analysis/*.Rmd")
html	0b9b87b	haiderinam	2020-04-02	Build site.
Rmd	fc5b9c0	haiderinam	2020-04-02	wflow_publish("analysis/*.Rmd")
html	2bce927	haiderinam	2020-04-02	Build site.
html	4ed9b35	haiderinam	2020-04-02	Build site.
Rmd	e31836a	haiderinam	2020-04-02	wflow_publish("analysis/*.Rmd")
html	99181d5	haiderinam	2020-04-02	Build site.
Rmd	17c01d4	haiderinam	2020-04-02	wflow_publish("analysis/index.Rmd")
html	1e2f469	haiderinam	2020-04-02	Build site.
html	e11eec5	haiderinam	2020-04-02	Build site.
Rmd	0053f96	haiderinam	2020-04-02	wflow_publish("analysis/*.Rmd")
html	b1cbbfa	haiderinam	2020-04-02	Build site.
Rmd	703346a	haiderinam	2020-04-02	Start workflowr project.

---

Duplex Sequencing Spike-Ins

• Click here for the script that reads BCRABL dose response data, and fits it to a 4-parameter dose response curve.
  

• Click here for the script that reads mutation annotation data and generates dataframes with annotated variants and the correct cell counts

• Click here for initial growth rate plots
  

• Click here for growth rate plots for ENU mutants
  

• Click here for analysis looking at whether we achieved our desired depth of coverages

• Click here for analysis looking at how well our data predicts BCRABL clinical abundance compared to conventional IC50s

• Click here for method to obtain confidence intervals on growth rates from IC50 measurements. Plotted alongside observed growth rate data, these confidence intervals show how well our pooled data matches predictions based off of IC50s. (Needs updates in methodology)
  

• Click here for analyses of replicate to replicate agreement between the spike in replicates. Also includes this analysis for the mutagenesis replicates. Also includes the agreement in observed vs predicted depth of coverages for all sequencing pools. Note: this analysis does not include dosage corrections that improves replicate to replicate heterogeneity.
  

• Click here to see analysis of predictions based on Enrich2 vs Shendure vs our method

• Click here for our dosing normalization strategy
  

• Click here for simulations showing enrichment and depletion events in a 3 mutant pool.

• Click here showing the conformity between the growth rates in the presence of drug measured at a low MAF via FACs, sequencing, and via IC50 studies for a single mutant.
  

• Click here to view BCRABL Imatinib heatmaps generated using CRISPR-cut libraries

• Click here to view preliminary BCRABL Imatinib and Asciminib heatmaps made with enzymatically sheared libraries

• Click here and to view iL3 independence data and here to view iL3 independence heatmap and here to view imatinib heatmaps on enzymatically sheared data

• Click here to view error rates without barcodes, with single strand consensi, and with duplex consensus sequencing.

• Click here to view the results of the BCRABL Library transduced in K562 Cells

• Click here to view analyses of the CDFs of our saturating mutagenesis libraries. These show how even or uneven the libraries are at different stages of the screening process.
  

• Click here to view analyses in which we compared base editing and saturating mutagenesis data on ABL. This is followed by analysis in which we decide on filter cutoffs for enrichment scores to detect signficantly depleting mutants that drop out for IL3 independence in BaF3s.
  

• Click here to view analyses in which we predicted admixtures of mutants made by sgRNAs in Base Editing Screens. We then used the saturating mutagenesis data to predict the fitness of these sgRNAs.
  

• Click here to view initial kinase function analyses.
  

• Click here to view our analyses of whether mutants in the cosmic/sanger database are resistant according to our screens.
  .

Click here to be redirected to the github page that contains all the data and analysis rmd files.

What is in each directory:

• Data: contains data downloaded prior to analyses.
  
• Output: contains data that the code makes
  
• Analysis: contains your Rmarkdown files with the code.
  
• Docs: contain the html output from the Rmd files in the analysis directory.
  
• Code: contains .R files that are functions that the Rmd files in the analysis folder use.