vcf2loci: Transform vcf to loci file
In Wedge-lab/dpclust3p: Dirichlet Process Clustering Pre-Processing Package

vcf2loci

R Documentation

Transform vcf to loci file

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

vcf2loci(
  vcf_files,
  fai_file,
  ign_file,
  outfile,
  dummy_alt_allele = NA,
  dummy_ref_allele = 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
`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)