GetChromosomeBAFs: Morphs phased SNPs from WGS input into haplotype blocks

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

Morphs phased SNPs from WGS input into haplotype blocks

Description

Morphs phased SNPs from WGS input into haplotype blocks

Usage

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.

Author(s)

dw9

Wedge-Oxford/battenberg documentation built on April 13, 2025, 5:15 a.m.