GetChromosomeBAFs: Morphs phased SNPs from WGS input into haplotype blocks
In Wedge-lab/battenberg: Battenberg subclonal copy number caller

GetChromosomeBAFs

R Documentation

Morphs phased SNPs from WGS input into haplotype blocks

Morphs phased SNPs from WGS input into haplotype blocks

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

`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.