get_map_qual: Retrieve mapping quality

In mmaitenat/ideafix: ideafix, DEAmination FIXing

Description

get_map_qual retrieves, for each C:G > T:A variant present in vcf_filename, the median Phred mapping quality (MAPQ) of the bases that support the alternate allele. This data is retrieved from vcf_filename.

Usage

get_map_qual(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.

Value

Numeric vector containing the MAPQ mapping quality of each C:G > T:A variant in vcf_filename, ordered by appearance in the file.

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