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 mfrkn/sequenza-pipeline

2. Download pipeline

git clone https://github.com/msfuji/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

Usage for multiple pairs of tumor/normals

This option is available only for users of the SHIROKANE supercomputer. Log in to OS7 nodes of SHIROKANE, and install cwltool.

qlogin -l os7
pip install cwlref-runner --user

Add the following command to ~/.bashrc.

export PATH=$PATH:~/.local/bin

1. Download pipeline

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

2. Prepare config files

• List BAM files of matched tumor/normals in sample.csv. Acceptable file format is a sample config file of Genomon2. Use [bam_import] to specify BAM files, and [mutation_call] to specify pairs of tumors and normals. Panel field of [mutation_call] is ignored.
• Specify file path for reference human genome GRCh37 as ref_fasta of genomon.cfg. Other fields are ignored.

3. Run pipeline

python scripts/start.py genomon.cfg sample.csv