write_battenberg_phasing: Writes the imputation and copy number phased haplotypes to a...
In Wedge-lab/battenberg: Battenberg subclonal copy number caller

write_battenberg_phasing

R Documentation

Writes the imputation and copy number phased haplotypes to a vcf

Description

Writes the imputation and copy number phased haplotypes to a vcf

Usage

write_battenberg_phasing(
  tumourname,
  SNPfiles,
  imputedHaplotypeFiles,
  bafsegmented_file,
  outprefix,
  chrom_names,
  include_homozygous = F
)

Arguments

`tumourname`	Sample name
`SNPfiles`	Character vector of the paths to the alleleFrequencies files, ordered by chromosome index
`imputedHaplotypeFiles`	Character vector of the paths to the impute_output files, ordered by chromosome index
`bafsegmented_file`	Path to the BAFSegmented file
`outprefix`	Prefix to write the output vcf files to
`chrom_names`	Names of the chromosomes
`include_homozygous`	Include homozygous SNPs in the output vcf file (Default = FALSE)