CODEX-nf

Pipeline for copy number variant calling from Whole Exome sequencing data using CODEX

Prerequisites

• R with package CODEX
• Rscript

and the following files:

• a bed file with the positions to consider
• a folder with Normal BAM files
• a folder with Tumor BAM files

Usage

nextflow run iarcbioinfo/CODEX-nf --dirNormal Normal --dirTumor Tumor --bedFile positions.bed --outdir output

Output

A series of files projectname_chromosome_optK_mode.txt, where chromosome takes its values in [1,2,...,22,X,Y], while projectname, optK, and mode are the same for all files. projectname and mode are specified by the user with options --project and --mode, respectively, and optK is computed by package CODEX.

All parameters

PARAMETER	DEFAULT	DESCRIPTION
--help	null	Print usage and parameters
--dirNormal	Normal	Path to Normal BAM files
--dirTumor	Tumor	Path to Tumor BAM files
--outdir	.	Path to output directiry
--bedFile	positions.bed	Path to bed file with positions to consider
--rem_from_bed	_random|chrUn|GL000209R|GL000191R|GL000194R	Strings to exclude from the bed file chromosome list
--project		Project name
--mem	5	Memory requested
--cpus	1	CPUs requested
--seg_mode	fraction	Mode for the segmentation algorithm (fraction or integer)