Morphs phased SNPs from WGS input into haplotype blocks

GetChromosomeBAFs(
  chrom,
  SNP_file,
  haplotypeFile,
  samplename,
  outfile,
  chr_names,
  minCounts = 1
)

Arguments

chrom: The chromosome number for which this function is called.
SNP_file: File containing allele counts for each SNP location.
haplotypeFile: File containing impute phasing output.
samplename: Name of the sample (used in header of output file).
outfile: Full path to where the output will be written.
chr_names: Names of all allowed chromosomes as a Vector.
minCounts: An integer describing the minimum number of reads covering this position to be included in the output.

dw9