Quick pull or explicitly calculate the VAF for mutation records of various flavors

Given a data.table or GenomicRanges VCF object, quickly extract or explicitly calculate the VAF for all mutations. For clarity, the read support for the VAF will be extracted as well. Currently supports somatic SNV/InDel VCFs from Mutect, Strelka, Varscan, SvABA, CaVEMan.

Usage

get_vaf(vcf_obj, caller, mut_type)

Arguments

vcf_obj: VCF file in data.table or GenomicRanges format
caller: Name of the caller that generated input VCF to be converted, supported: mutect, strelka, varscan, svaba, caveman
mut_type: Type of mutations within VCF, supported: snv, indel

Value

data.table object with read support and VAF per record