input_known_haplotypes: Combine imputation results with external haplotype blocks

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

Combine imputation results with external haplotype blocks

Description

Combine imputation results with external haplotype blocks

Usage

input_known_haplotypes(
  chrom_names,
  chrom,
  imputedHaplotypeFile,
  externalHaplotypeFile = NA,
  oldfilesuffix = "_noExt.txt"
)

Arguments

chrom_names	Names of the chromosomes
chrom	chromosome for which to reconstruct haplotypes
imputedHaplotypeFile	Full path to the imputed haplotyope file for the indexed chromosome
externalHaplotypeFile	Full path to the vcf containing haplotype blocks for the indexed chromosome (Default: NA)
oldfilesuffix	Suffix to be added to the original imputedHaplotypeFile (Default: _noExt.txt)

Author(s)

jdemeul

Wedge-lab/battenberg documentation built on April 5, 2025, 9:15 a.m.