array2vcf: SNP array to VCF

In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

SNP array to VCF

Description

Converts output from Genome Studio (Final Report or Wide) to VCF

Usage

array2vcf(array.file, map.file, model.file = NULL, ploidy, vcf.file)

Arguments

array.file	name of input file with SNP array allele intensities
map.file	vcf file with map positions for the markers
model.file	normal mixture model parameters for genotype calls
ploidy	sample ploidy, for use with model.file
vcf.file	output vcf file

Details

Auto-detects whether the input file is a Genome Studio Final Report, which is a "long" format with 9-row header, or in "wide" format, where all the data for each marker is one row. XY values are multiplied by 100

Genotype calls will attempt to be imported from the GS Final Report when model.file=NULL. For diploids, columns named "Allele 1 - AB" and "Allele 2 - AB" are expected. For tetraploids, a single column named "Alleles - AB" is expected.

It is assumed that the parameters in model.file lead to genotype calls for the dosage of allele B. For a VCF file, genotype calls need to be based on the dosage of ALT. By default, it is assumed that A is the REF allele. For variants where B is REF, include "REF=B" as INFO in the VCF map.file.

jendelman/polyBreedR documentation built on Jan. 5, 2025, 12:13 a.m.