GetChromosomeBAFs_SNP6: Morphs phased SNPs from SNP6 input into haplotype blocks

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

Morphs phased SNPs from SNP6 input into haplotype blocks

Description

This function matches allele frequencies and halplotype info, reverses frequencies by haplotype, combines the output and saves it to disk.

Usage

GetChromosomeBAFs_SNP6(
  chrom,
  alleleFreqFile,
  haplotypeFile,
  samplename,
  outputfile,
  chr_names
)

Arguments

chrom	The chromosome number for which this function should run.
alleleFreqFile	File containing allele frequency information.
haplotypeFile	File containing haplotype information.
samplename	Identifier for the sample (used in header of output file).
outputfile	Full path pointing to where output should be written.
chr_names	Vector of chromosome names

Author(s)

dw9

Wedge-Oxford/battenberg documentation built on Aug. 4, 2023, 6:27 p.m.