Combine imputation results with external haplotype blocks — input_known_haplotypes • Battenberg

Combine imputation results with external haplotype blocks

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

jdemeul