Format and subset genotype data from a VCF file.

Extract numeric alleles from vcf object and filter out SNPs missing genotype data or outside the Minor Allele Frequency range in `SplatPopParams`.

Usage

splatPopParseVCF(vcf, params)

Arguments

vcf

VariantAnnotation object containing genotypes of samples.

params

SplatPopParams object containing parameters for population scale simulations. See SplatPopParams for details.

Value

Genotype data.frame