Sequenza-pipeline

Analyze somatic copy number alteration of tumor using Sequenza. WGS/WES BAM files of matched tumor and normal are analyzed.

Requirements

• cwltool
• Docker or Singularity

Usage for a single pair of tumor/normal

1. Pull docker image from Docker Hub.

docker pull waszaklab/sequenza-pipeline:v0.9

2. Download pipeline

git clone https://github.com/waszaklab/Sequenza-pipeline.git
cd Sequenza-pipeline

3. Prepare config file

Specify sample ID, tumor BAM, normal BAM, reference FASTA, and the number of threads for computation in a YAML-format config file. See example/sequenza-command.yaml.

4. Run pipeline

cwl-runner sequenza-command.cwl config.yaml