write_battenberg_phasing: Writes the imputation and copy number phased haplotypes to a...

In Wedge-Oxford/battenberg: Battenberg subclonal copy number caller

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)

Author(s)

jdemeul

Wedge-Oxford/battenberg documentation built on Aug. 4, 2023, 6:27 p.m.