run_haplotyping: Construct haplotypes for a chromosome

In shaghayeghsoudi/Battenberg_customized: Battenberg subclonal copy number caller

Description

This function takes preprocessed data and performs haplotype reconstruction.

Usage

run_haplotyping(
  chrom,
  tumourname,
  normalname,
  ismale,
  imputeinfofile,
  problemloci,
  impute_exe,
  min_normal_depth,
  chrom_names,
  snp6_reference_info_file = NA,
  heterozygousFilter = NA
)

Arguments

chrom	The chromosome for which to reconstruct haplotypes
tumourname	Identifier of the tumour, used to match data files on disk
normalname	Identifier of the normal, used to match data files on disk
ismale	Boolean, set to TRUE if the sample is male
imputeinfofile	Full path to the imputeinfo reference file
problemloci	Full path to the problematic loci reference file
impute_exe	Path to the impute executable (can be found if its in $PATH)
min_normal_depth	Minimal depth in the matched normal required for a SNP to be used
chrom_names	A vector containing the names of chromosomes to be included
snp6_reference_info_file	SNP6 only parameter Default: NA
heterozygousFilter	SNP6 only parameter Default: NA

Author(s)

sd11

shaghayeghsoudi/Battenberg_customized documentation built on Feb. 13, 2022, 4:10 a.m.