filter_MAPQ: Filter MAPQ

In andygxzeng/ECSI: Espresso - Somatic Mutation Calling using Contextual Error Models

Description

Filter variants to keep those that are equal to or greater than a MAPQ cutoff.

Usage

filter_MAPQ(sample, MAPQ_cutoff = 59)

Arguments

sample	VRanges object of the varscan pileup2cns output
MAPQ_cutoff	Minimum acceptable MAPQ score. Default is 59

Value

This function returns a VRanges object filtered by MAPQ cutoff

Examples

## Not run: 
variants <- filter_MAPQ(sample = variants, MAPQ_cutoff = 59)

## End(Not run)

andygxzeng/ECSI documentation built on Feb. 6, 2021, 8:53 a.m.