updog2vcf: Export Updog Results as VCF

In BIGr: Breeding Insight Genomics Functions for Polyploid and Diploid Species

Export Updog Results as VCF

Description

This function will convert an Updog output to a VCF file

Usage

updog2vcf(
  multidog.object,
  output.file,
  updog_version = NULL,
  RefAlt = NULL,
  compress = TRUE
)

Arguments

multidog.object	updog output object with class "multidog" from dosage calling
output.file	output file name and path
updog_version	character defining updog package version used to generate the multidog object
RefAlt	optional data frame with four columns named "Chr", "Pos", "Ref", and "Alt" containing the reference and alternate alleles for each SNP in the same order as in the multidog object
compress	logical. If TRUE returns a vcf.gz file

Details

When performing dosage calling for multiple SNPs using Updog, the output file contains information for all loci and all samples. This function will convert the updog output file to a VCF file, while retaining the information for the values that are commonly used to filter low quality and low confident dosage calls.

Value

A vcf file

References

Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping polyploids from messy sequencing data. Genetics, 210(3), 789-807.

Examples

# Retrieving the updog output multidog object
load(system.file("extdata", "iris-multidog.rdata", package = "BIGr"))

temp_file <- tempfile()

# Convert updog to VCF, where the new VCF will be saved at the location specified in the output.file
updog2vcf(
  multidog.object = mout,
  output.file = temp_file,
  updog_version = "0.0.0",
  compress = TRUE
)

#Removing the example vcf
rm(temp_file)

BIGr documentation built on Nov. 5, 2025, 6:03 p.m.