SplitOneMutectVCF: Split a mutect2 VCF into SBS, DBS, and ID VCFs, plus a list...

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

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)

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.

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

ICAMS documentation built on April 3, 2021, 5:07 p.m.