prepare_wgs: Prepare WGS data for haplotype construction
In Wedge-Oxford/battenberg: Battenberg subclonal copy number caller

prepare_wgs

R Documentation

Prepare WGS data for haplotype construction

Description

This function performs part of the Battenberg WGS pipeline: Counting alleles, constructing BAF and logR and performing GC content correction.

Usage

prepare_wgs(
  chrom_names,
  tumourbam,
  normalbam,
  tumourname,
  normalname,
  g1000allelesprefix,
  g1000prefix,
  gccorrectprefix,
  repliccorrectprefix,
  min_base_qual,
  min_map_qual,
  allelecounter_exe,
  min_normal_depth,
  nthreads,
  skip_allele_counting,
  skip_allele_counting_normal = F
)

Arguments

`chrom_names`	A vector containing the names of chromosomes to be included
`tumourbam`	Full path to the tumour BAM file
`normalbam`	Full path to the normal BAM file
`tumourname`	Identifier to be used for tumour output files
`normalname`	Identifier to be used for normal output files
`g1000allelesprefix`	Prefix path to the 1000 Genomes alleles reference files
`g1000prefix`	Prefix path to the 1000 Genomes SNP reference files
`gccorrectprefix`	Prefix path to GC content reference data
`repliccorrectprefix`	Prefix path to replication timing reference data (supply NULL if no replication timing correction is to be applied)
`min_base_qual`	Minimum base quality required for a read to be counted
`min_map_qual`	Minimum mapping quality required for a read to be counted
`allelecounter_exe`	Path to the allele counter executable (can be found in $PATH)
`min_normal_depth`	Minimum depth required in the normal for a SNP to be included
`nthreads`	The number of paralel processes to run
`skip_allele_counting`	Flag, set to TRUE if allele counting is already complete (files are expected in the working directory on disk)
`skip_allele_counting_normal`	Flag, set to TRUE from the second sample onwards for multisample case (Default: FALSE)