GenerateDPinput_strelka_vcf: Generate DP input for strelka vcfs, using tier 1 snvs

In afrangou/CleanCNA: Calling and recalling subclonal copy number using SNP and SNV information to provide a high quality set of copy number profiles.

Description

Converts snv counts from vcf into input format for DPClust

Usage

GenerateDPinput_strelka_vcf(
  tumourplatekey,
  normalplatekey,
  gender,
  vcffilepath,
  rhoandpsifilepath,
  subcloneshg38filepath,
  output_loci_file,
  output_file,
  output_DPinput_file
)

Arguments

Loci	of SNP positions used in CNV call Allele frequencies of same SNP positions File containing purity and ploidy of tumour sample Subclones file from Battenberg containing copy number segments across genome Sex of patient

Value

A file containing all snv loci, their mutation copy number status, and their CCF (cancer cell fraction)

afrangou/CleanCNA documentation built on Dec. 28, 2021, 8:21 p.m.