get_SB: Calculate strand bias

In mmaitenat/ideafix: ideafix, DEAmination FIXing

Description

This function calculates, for each C:G > T:A variant present in vcf_filename, two strand bias (SB) metrics: SB defined by GATK (SB-GATK) and SB defined by Guo et. al. (SB-Guo). The calculation is based on data retrieved from vcf_filename.

Usage

get_SB(vcf_filename, 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.
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

See calc_SB_Guo and calc_SB_GATK for further detail on these SB values.

Value

List of two numeric vectors. Each element in the vectors corresponds to a C:G > T:A variant in vcf_filename. The elements are ordered by appearance in vcf_filename. The first vector stores SB-GATK values and the second one SB-Guo values.

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