get_ref_bases: Retrieve number of reference alleles

In mmaitenat/ideafix: ideafix, DEAmination FIXing

Description

This function retrieves the number of reads that support the reference allele of each C:G > T:A variant present in vcf_filename. This data is retrieved from vcf_filename.

Usage

get_ref_bases(vcf_filename, depth, samplename, ...)

Arguments

vcf_filename	character string naming the path to the input vcf, i.e. the vcf file containing the variants to classify. This file must have been generated with Mutect2, either in tumor only or tumor/normal mode with strand bias annotation enabled.
depth	numeric vector containing the read depth at each C:G > T:A variant locus
samplename	character string naming the sample in vcf_filename. This must match the name given to the sample when running Mutect2. It can be obtained by calling get_samplename on vcf_filename.
...	additional arguments not to be checked.

Details

get_ref_bases first retrieves the number of reads that support the reference allele of each C:G > T:A variant present in vcf_filename. It then calculates the ratio between this value and the total number of reads at the site and reports both values, which is provided in depth.

Value

List containing two numeric vectors: the number of reads that support the reference allele and the number of reads that support the reference allele divided by the total number of reads at that site. Each element in the vectors corresponds to a C:G > T:A variant in vcf_filename and the elements are ordered by appearance in vcf_filename.

mmaitenat/ideafix documentation built on Sept. 18, 2021, 7:55 a.m.