This repository contains code to run a modified version of QDNAseq on shallow WGS, on WXS and on targeted sequencing data.
Whole genome sequencing requires these parameters:
Rscript call_copynumber.R [samplename] [tumourbam] [normalname] [normalbam]
Whole exome sequencing - where the offtarget reads are used - takes an extra parameter which is a bed file specifying the regions that were targeted, i.e. all exons in the genome
Rscript call_copynumber_exome.R [samplename] [tumourbam] [normalname] [normalbam] [targetregions]
Targeted sequencing - where offtarget reads are used - takes an extra parameter which is a bed file specifying the regions that were targeted
Rscript call_copynumber_offtarget.R [samplename] [tumourbam] [normalname] [normalbam] [targetregions]
- A slightly modified version of QDNAseq from here: https://github.com/sdentro/QDNAseq/tree/dev
R -q -e 'devtools::install_github("sdentro/QDNAseq", ref="dev")'