ITH_nf

In development - do not use

Description

Perform Intra-Tumor Heterogeneity (ITH) analysis.

Dependencies

1. This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines. 2.Strelka2: see official installation here. ) 3.Platypus: see official installation here. 4.Bcftools: see official installation here. 5.Tabix: see official installation here. 6.Falcon: see official installation here. 7.Canopy: see official installation here.

Input

Name	Description
--bam_folder	Folder containing BAM files
--output_folder	Path to output folder
--strelka	Path to strelka installation dir
--correspondance	File containing the correspondance between the normal and two tumor samples and the sample
--ref	Reference file
--regions	Regions
--lib	Path to libraries : falcon.output.R falcon.output.R falcon.getASCN.epsilon.R custom_canopy.plottree.R
--K	Number of subclones to generate by Canopy
--tabix	Path to tabix installation dir
--platypus	Path to platypus installation dir
--Rcodes	Path to folder containing R codes

Flags

Flags are special parameters without value.

Name	Description
--help	Display help

Usage

nextflow run iarcbioinfo/pipeline.nf --bam_folder path/to/bams/ --correspondance path/to/correpondance/csv/ --output_folder /path/to/output --strelka /path/to/trelka --bcftools /path/to/bcftools --tabix /path/to/tabix --platypus /path/to/platypus --Rcodes --lib /path/to/R/libraries --K integer --ref /path/to/ref --regions path/to/regions

Output

Name	Description
VCFs (and corresponding .tbi)	Results of the germline and somatic callings, the somatic and germline coverage
PDFs	Reports for Falcon and Canopy runs
rda	Falcon and Canopy coordinates
txt	Standard error for Falcon
SVGs	Canopy trees