This repository contains a Biowdl workflows which uses Haplotypecaller to perform variantcalling.
You can find the documentation here
This workflow is part of Biowdl, developed by the SASC team at Leiden University Medical Center.
java -Dconfig.file=docker_slurm.conf -jar /apps/cromwell/cromwell-53.1.jar run multisample-variantcalling.wdl -i tests/integration/single_sample_gvcf.json -o gatk-variantcalling.options.json