dumpCounts.StrelkaIndel: Dump allele counts from vcf - Strelka indel pipeline

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

Dump allele counts from vcf - Strelka indel pipeline

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. There are no counts for the matched normal.

Usage

dumpCounts.StrelkaIndel(
  vcf_infile,
  tumour_outfile,
  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
refence_genome	Optional parameter specifying the reference genome build used
dummy_alt_allele	Specify allele to be used to encode the alt counts (the indel can be multiple alleles)
dummy_ref_allele	Specify allele to be used to encode the ref counts (the indel can be multiple alleles)

Author(s)

sd11

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