PCAWG_read_table_and_evaluate_DBS: Read a table that specifies how to process VCFs and mini-BAMS...

In steverozen/DBSverify: Analyze Next Generation Sequencing Data to Verify Somatic Double-BaseSubstituion (DBS) Calls

Description

Read a table that specifies how to process VCFs and mini-BAMS to evaluate DBS calls, for PCAWG Collaboratory data.

Usage

PCAWG_read_table_and_evaluate_DBS(
  in.table,
  in.vcf.dir,
  minibam.dir,
  out.vcf.dir = in.vcf.dir,
  bam.suffix = "_dbs_srt",
  verbose = 1
)

Arguments

in.table	the file path of the table to process; in production, .../DBSverify/data-raw/collaboratory_bams_full_2021_07_13.csv, for testing .../DBSverify/data-raw/short_collaboratory_bams.csv.
in.vcf.dir	The path to the directory containing the DBS VCF files.
minibam.dir	The path to the directory containing the mini BAMs.
out.vcf.dir	The path to the directory in which to put the "evaluated" DBS VCF files.
bam.suffix	String to add to end of BAM file name; depends on the conventions used by the script (run on the Collaboratory) that generated the miniBAMs.
verbose	If > 0 generate some progress messages.

Details

This is a specialized function for processing PCAWG data from the ICGC (International Cancer Genome) "Collaboratory" cloud computing system, once the miniBAMs have been created in the Collaboratory and downloaded. The in.table and associated BED files were used to specify the contents of the miniBAMs. The result consists of the "evaluated" DBS VCF files. The naming of the input and output VCF files and the mini BAMs is governed by the contents of in.table, with the VCF file names incorporating the "aliquot_id" and the miniBAM names based on the icgc_donor_id and the T_Specimen ID and N_Specimen ID.

steverozen/DBSverify documentation built on Dec. 23, 2021, 5:34 a.m.