gen2vcf: Convert IMPUTE2 gen to VCFv4.1 format, input for fastqtl

In oncogenetics/oncofunco: Custom function for Oncogenetics team

Convert IMPUTE2 gen to VCFv4.1 format, input for fastqtl

Description

This function converts IMPUTE2 gen file posterior probabilities to dosage, then outputs to VCF file.

Usage

gen2vcf(
  genFile,
  sampleFile,
  chrName,
  outVCFFile,
  outVCFHeader = "##fileformat=VCFv4.1",
  subsetSNPs = NULL,
  subsetSamples = NULL
)

Arguments

genFile	input gen file
sampleFile	if provided sampleID will be added as header, else X1..Xn as sampleID
chrName	chromosome name c(1:22,X,Y)
outVCFFile	output file name for VCF
outVCFHeader	output VCF header lines
subsetSNPs	index of SNPs to subset - rows
subsetSamples	index of Samples to subset - coloumns

Value

outputs VCF file, nothing returned in the workspace

Author(s)

Tokhir Dadaev

oncogenetics/oncofunco documentation built on March 9, 2024, 5:23 p.m.