calc_SB_Guo: Calculate Guo strand bias

In mmaitenat/ideafix: ideafix, DEAmination FIXing

Description

This function calculates variant strand bias as defined by Guo et. al. (SB-Guo).

Usage

calc_SB_Guo(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 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-Guo value of the variant.

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