heterozygosity {vcfppR}

calculate the number of heterozygous SNPs for each sample

Description

calculate the number of heterozygous SNPs for each sample

Usage

heterozygosity(vcffile, region = "", samples = "-", pass = FALSE, qual = 0)

Arguments

vcffile

path to the VCF file with index

region

region to extract, default "" for all

samples

samples to extract, default "-" for all

pass

restrict to variants with FILTER==PASS

qual

restrict to variants with QUAL > qual.

Value

A list of heterozygosity couts for each sample along with its id in the vcf header