Read_SBS_VCF_and_BAMs_to_verify_DBSs: Aggressively merge SBSs into DBSs then determine whether...

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

Description

Aggressively merge SBSs into DBSs then determine whether sequencing reads in fact support DBSs.

Usage

Read_SBS_VCF_and_BAMs_to_verify_DBSs(
  input.vcf,
  Nbam.name,
  Tbam.name,
  variant.caller,
  N.slice.dir = tempfile(),
  T.slice.dir = tempfile(),
  unlink.slice.dir = TRUE,
  outfile = NULL,
  verbose = 0
)

Arguments

input.vcf	If a character string, then the path to a VCF file; otherwise A a single VCF "file" as a data.frame or similar object.
Nbam.name	The name of the BAM file for the normal sample corresponding to vcf.name.
Tbam.name	The name of the BAM file for the tumor sample corresponding to vcf.name.
variant.caller	One of "strelka", "PCAWG", or "unknown". Merging adjacent SBS is done by ReadAndSplitVCFs in the ICAMS package.
N.slice.dir	Directory for the slices of the normal BAM. Created if necessary.
T.slice.dir	Directory for the slices of the tumor BAM. Created if necessary. Must be different than N.slice.dir.
unlink.slice.dir	If TRUE unlink N.slice.dir and T.slice.dir before return.
outfile	If not NULL then write the "evaluated" VCF to outfile; otherwise write it to paste0(input.vcf(vcf.name, "_evaluated.vcf"). Must be non-NULL if input.vcf is not a file path.
verbose	If > 0 print a message when starting the number of slices generated every verbose slices.

Details

Note: argument input.vcf must be a file path. This function creates a new VCF file. See Read_DBS_VCF_and_BAMs_to_verify_DBSs for details.

Value

Same as Read_DBS_VCF_and_BAMs_to_verify_DBSs.

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