Snakemake workflow: dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.

Authors

• Johannes Köster (https://koesterlab.github.io)

Usage

Step 1: Install workflow

If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further develop this workflow, fork this repository. Please consider providing any generally applicable modifications via a pull request.

In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).

Step 2: Configure workflow

Configure the workflow according to your needs via editing the file config.yaml.

Step 3: Execute workflow

Test your configuration by performing a dry-run via

snakemake -n

Execute the workflow locally via

snakemake --cores $N

using $N cores or run it in a cluster environment via

snakemake --cluster qsub --jobs 100

or

snakemake --drmaa --jobs 100

See the Snakemake documentation for further details and other options (e.g. Cloud execution).

Step 4: Investigate results

After successful execution, you can create a self-contained report with all results via:

snakemake --report report.html

Example output from our test dataset can be seen here.

Testing

Tests cases are in the subfolder .test. They should be executed via continuous integration with Travis CI.