Variant Calling Pipeline for Cancer Genome Sequencing

$ pip install -U \
  https://github.com/dceoy/sagvc/archive/main.tar.gz \
  https://github.com/dceoy/vcline/archive/master.tar.gz

Dependent commands:

• pigz
• pbzip2
• bgzip
• tabix
• samtools
• bedtools
• bcftools
• java
• gatk
• cutadapt
• fastqc
• trim_galore
• bwa or bwa-mem2
• python (Python 3)
• python2
• configManta.py
• configureStrelkaSomaticWorkflow.py
• configureStrelkaGermlineWorkflow.py
• delly
• R
• Rscript
• cnvkit.py
• msisensor-pro
• snpEff (java -jar /path/to/snpEff.jar)
• vep

Pull the image from Docker Hub.

$ docker image pull dceoy/vcline

1. Download and process resource data.

   $ vcline download --dest-dir=/path/to/download/dir

2. Create vcline.yml.

   $ vcline init
   $ vi vcline.yml     # => edit configurations

3. Run the pipeline.

   $ vcline run --workers=2

Run vcline --help for more information.