MQRankSum: Plot MappingQualityRankSumTest (MQRankSum)

In Hatoonli/vcfqc: What the Package Does (One Line, Title Case)

Plot MappingQualityRankSumTest (MQRankSum)

Description

This is the u-based z-approximation from the Rank Sum Test for mapping qualities. It compares the mapping qualities of the reads supporting the reference allele and the alternate allele. A positive value means the mapping qualities of the reads supporting the alternate allele are higher than those supporting the reference allele; a negative value indicates the mapping qualities of the reference allele are higher than those supporting the alternate allele. A value close to zero is best and indicates little difference between the mapping qualities.

Usage

MQRankSum(f, n)

Arguments

f	VCF input file
n	Threshold value (optional), default is the recommended GATK value.

Value

A plot of MQRankSum score and frequency with table summary and number of variants falling outside the threshold

Hatoonli/vcfqc documentation built on May 16, 2022, 12:19 p.m.