Writes the imputation and copy number phased haplotypes to a vcf

Source: R/haplotype_external.R

Writes the imputation and copy number phased haplotypes to a vcf

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

jdemeul