dpIn2vcf: DPClust input file to vcf

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

DPClust input file to vcf

Description

Transform a dirichlet input file into a VCF with the same info. It filters out mutations in areas that are not contained in the supplied genome index (fai file) or are contained in the ignore file (ign file) It takes the DP input file created by runGetDirichletProcessInfo and combines the columns with the vcf file supplied. Finally it gzips and indexes the file

Usage

dpIn2vcf(
  vcf_infile,
  dpIn_file,
  vcf_outfile,
  fai_file,
  ign_file,
  genome = "hg19"
)

Arguments

vcf_infile	Filename of the VCF file to use as a base
dpIn_file	Filename of a DP input file
vcf_outfile	Filename of the output file
fai_file	Path to a reference genome index containing chromosome names
ign_file	Path to a file containing contigs to ignore
genome	Specify the reference genome for reading in the VCF

Author(s)

sd11

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