run_haplotyping: Construct haplotypes for a chromosome
In Wedge-lab/battenberg: Battenberg subclonal copy number caller

run_haplotyping

R Documentation

Construct haplotypes for a chromosome

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,
  externalhaplotypeprefix = NA,
  use_previous_imputation = F,
  snp6_reference_info_file = NA,
  heterozygousFilter = NA,
  usebeagle = FALSE,
  beaglejar = NA,
  beagleref = NA,
  beagleplink = NA,
  beaglemaxmem = 10,
  beaglenthreads = 1,
  beaglewindow = 40,
  beagleoverlap = 4,
  javajre = "java"
)

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
`usebeagle`	Should use beagle5 instead of impute2 Default: FALSE
`beaglejar`	Full path to Beagle java jar file Default: NA
`beagleref`	Full path to Beagle reference file Default: NA
`beagleplink`	Full path to Beagle plink file Default: NA
`beaglemaxmem`	Integer Beagle max heap size in Gb Default: 10
`beaglenthreads`	Integer number of threads used by beagle5 Default:1
`beaglewindow`	Integer size of the genomic window for beagle5 (cM) Default:40
`beagleoverlap`	Integer size of the overlap between windows beagle5 Default:4
`javajre`	Path to the Java JRE executable (default java, i.e. in $PATH)