get_base_qual: Retrieve base quality

In mmaitenat/ideafix: ideafix, DEAmination FIXing

Description

This function retrieves the median Phred quality of the bases that support the alternate allele of each C:G > T:A variant present in vcf_filename. This data is retrieved from vcf_filename.

Usage

get_base_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.

Details

get_base_qual first retrieves the median Phred quality of the bases that support the alternate allele of each C:G > T:A variant present in vcf_filename. It then retrieves this same value for the bases that support the reference allele of the same set of variants. It finally calculates the ratio between the two of them and reports two values: the median Phred quality of the bases that support the alternate allele and the calculated ratio.

Value

List containing two numeric vectors: the median Phred base quality of the alternate allele and the ratio between the median Phred base quality of the alternate allele and the median Phred base quality of the reference allele. Each element in the vectors corresponds to a C:G > T:A variant in vcf_filename and the elements are ordered by appearance in vcf_filename.

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