ICAMS (version 3.0.11)

SplitOneMutectVCF: Split a mutect2 VCF into SBS, DBS, and ID VCFs, plus a list of other mutations

Description

Split a mutect2 VCF into SBS, DBS, and ID VCFs, plus a list of other mutations

Usage

SplitOneMutectVCF(vcf.df, name.of.VCF = NULL, chr.names.to.process = NULL)

Value

A list with 3 in-memory VCFs and discarded variants that were not incorporated into the first 3 VCFs:

* SBS: VCF with only single base substitutions.

* DBS: VCF with only doublet base substitutions as called by Mutect.

* ID: VCF with only small insertions and deletions.

* discarded.variants: Non-NULL only if there are variants that were excluded from the analysis. See the added extra column

discarded.reason for more details. @md

Arguments

vcf.df

An in-memory data.frame representing a Mutect VCF, including VAFs, which are added by ReadMutectVCF.

name.of.VCF

Name of the VCF file.

chr.names.to.process

A character vector specifying the chromosome names in VCF whose variants will be kept and processed, other chromosome variants will be discarded. If NULL(default), all variants will be kept except those on chromosomes with names that contain strings "GL", "KI", "random", "Hs", "M", "JH", "fix", "alt".