calc_SB_GATK: Calculate GATK strand bias

In mmaitenat/ideafix: ideafix, DEAmination FIXing

Description

This function calculates variant strand bias as defined by GATK (SB-GATK).

Usage

calc_SB_GATK(a, b, e, d)

Arguments

a	Number of reads supporting the reference allele mapping to the forward strand.
b	Number of reads supporting the alternate allele mapping to the forward strand.
e	Number of reads supporting the reference allele mapping to the forward strand.
d	Number of reads supporting the alternate allele mapping to the reverse strand.

Details

This strand bias value was defined by GATK and described in The effect of strand bias in Illumina short-read sequencing data. It can be accessed here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532123/. It ranges from 0 to infinity.

Value

Numeric element with the SB-GATK value of the variant.

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