mut_cn_phasing: Phase mutation to SNP/copy number

In shaghayeghsoudi/DPclust3p_Customised: Dirichlet Process Clustering Pre-Processing Package

Phase mutation to SNP/copy number

Description

Run mutation to copy number phasing. This function requires the Linkage_pull.pl script in $PATH. Note: This function should either be run separately per chromosome and then combined with concat_files or on all chromsomes in one go, but then the _allHaplotypeInfo.txt Battenberg files need to be concatenated first.

Usage

mut_cn_phasing(
  loci_file,
  phased_file,
  hap_file,
  bam_file,
  bai_file,
  outfile,
  max_distance
)

Arguments

loci_file	A list of loci
phased_file	The .BAFsegmented.txt output file from Battenberg
hap_file	Path to the _allHaplotypeInfo.txt Battenberg output file to be used
bam_file	Full path to the bam file
bai_file	Full path to the bai file
outfile	File to save the output
max_distance	The max distance of a mutation and SNP can be apart to be considered for phasing

Author(s)

sd11, dw9

shaghayeghsoudi/DPclust3p_Customised documentation built on March 18, 2022, 5:28 a.m.