dumpCounts.Broad: Dump allele counts from vcf - Broad ICGC pancancer pipeline

In Wedge-lab/dpclust3p: Dirichlet Process Clustering Pre-Processing Package

Dump allele counts from vcf - Broad ICGC pancancer pipeline

Description

Dump allele counts stored in the sample columns of the VCF file. Output will go into a file supplied as tumour_outfile and optionally normal_outfile. It will be a fully formatted allele counts file as returned by alleleCounter.

Usage

dumpCounts.Broad(
  vcf_infile,
  tumour_outfile,
  normal_outfile = NA,
  refence_genome = "hg19",
  samplename = NA
)

Arguments

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

Author(s)

sd11

Wedge-lab/dpclust3p documentation built on June 14, 2025, 4:24 p.m.