maf2loci: Transform vcf to loci file

In shaghayeghsoudi/DPclust3p_Customised: Dirichlet Process Clustering Pre-Processing Package

Transform vcf to loci file

Description

Function that dumps the loci of snvs from a series of vcf files into a single loci file

Usage

maf2loci(maf_file, outfile, dummy_alt_allele = NA, dummy_ref_allele = NA)

Arguments

outfile	Where to store the output
dummy_alt_allele	The alt allele to store, supply when you want to override what is in the VCF (Default: NA)
dummy_ref_allele	The reference allele to store, supply when you want to override what is in the VCF (Default: NA)
vcf_files	A vector of vcf files to be considered
fai_file	Reference genome index
ign_file	A file with chromosomes to be excluded from consideration

Author(s)

sd11

shaghayeghsoudi/DPclust3p_Customised documentation built on March 18, 2022, 5:28 a.m.