VerifyDBSVcf: Given a VCF and the locations of a tumor and normal BAM files...

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

Description

Given a VCF and the locations of a tumor and normal BAM files check whether analysis of individual reads supports DBSs calls.

Usage

VerifyDBSVcf(
  vcf,
  Nbam.name,
  Tbam.name,
  N.slice.dir,
  T.slice.dir,
  padding = 10,
  verbose = 0
)

Arguments

vcf	An in-memory representation of a "variant call file", VCF, as a data.frame.
Nbam.name	The name of the BAM file for the normal sample.
Tbam.name	The name of the BAM file for the tumor sample.
N.slice.dir	The directory containing the slices of the normal BAM.
T.slice.dir	The directory containing the slices of the tumor BAM. Must be different than N.slice.dir.
padding	The number of base pairs on either side of the first position of the DBS to include in the slices.
verbose	If > 0 print a message when starting the number of slices generated every verbose slices.

Value

An in-memory VCF based on the input vcf with the additional columns as described in Read_DBS_VCF_and_BAMs_to_verify_DBSs.

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