genSnpZygosity: Simplifies the SNP Zygosity from MuTect

In quevedor2/WadingPool: A toolkit for shallow/low-pass whole genome sequencing analysis

Description

Takes a single sample Mutect VCF that has force called all dbSNP sites and reduces it to a single column of 1,2,3 values corresponding to REF.HOMOZYGOUS, HETEROZYGOUS, and ALT.HOMOZYGOUS respectively using Perl. If multiple samples are given, it will concatenate the samples into a single matrix.

Usage

genSnpZygosity(
  sampleid,
  caller = "GATK",
  chrs = paste0("chr", c(1:22, "X", "Y"))
)

Arguments

sampleid	Vector of sample IDs for the filename [chr].[sampleid].vcf
caller	Either 'Mutect' or 'GATK' (collectAllelicCounts)
chrs	Chrs for the filename [chr].[sampleid].vcf

Value

Matrix of parsed output values

quevedor2/WadingPool documentation built on Dec. 22, 2021, 10:59 a.m.