VCF2dosage: Convert VCF to dosage file

In jendelman/GWASpoly: Genome-wide Association Studies for Autopolyploids

Convert VCF to dosage file

Description

Convert VCF to dosage file

Usage

VCF2dosage(
  VCF.file,
  dosage.file,
  geno.code,
  ploidy,
  samples = NULL,
  min.DP = 1,
  max.missing,
  min.minor = 5
)

Arguments

VCF.file	VCF filename (can be gzipped)
dosage.file	CSV filename to output with allele dosage
geno.code	genotype code in the FORMAT field: "GT" of "DS"
ploidy	ploidy
samples	optional vector of sample names, to export subset of the population
min.DP	minimum per sample depth (DP) to export genotype. Default is 1, for no filtering.
max.missing	threshold for missing data per marker, as a proportion.
min.minor	minimum number of samples with the minor allele. Default is 5.

Details

Only bi-allelic variants supported. The "GT" option for geno.code is the posterior maximum genotype (e.g., 0/0/1/1). "DS" represents the posterior mean dosage of the alternate allele. VCF file must conform to 4.1 or later.

jendelman/GWASpoly documentation built on Oct. 16, 2024, 5:59 a.m.