dumpCounts.scalpel: Dump allele counts from vcf - Scalpel
In Wedge-lab/dpclust3p: Dirichlet Process Clustering Pre-Processing Package

dumpCounts.scalpel

R Documentation

Dump allele counts from vcf - Scalpel

Description

Dump allele counts stored in the info column of the VCF file. Output will go into a file supplied as tumour_outfile. It will be a fully formatted allele counts file as returned by alleleCounter.

Usage

dumpCounts.scalpel(
  vcf_infile,
  tumour_outfile,
  samplename,
  normal_outfile = NA,
  refence_genome = "hg19",
  dummy_alt_allele = NA,
  dummy_ref_allele = NA
)

Arguments

`vcf_infile`	The vcf file to read in
`tumour_outfile`	File to save the tumour counts to
`samplename`	Parameter specifying the samplename to be used for matching the right column in the VCF
`normal_outfile`	Optional parameter specifying where the normal output should go
`refence_genome`	Optional parameter specifying the reference genome build used