Awesome
ITH_nf
In development - do not use
Description
Perform Intra-Tumor Heterogeneity (ITH) analysis.
Dependencies
- 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 |