This repository contains the Biowdl workflow usable for processing germline-DNA data. Starting with FASTQ files and resulting in VCF files. Can switch between joint genotyping and single sample calling modes. It can also call the X and Y chromosomes with the correct ploidy if given BED files for the non-PAR regions.
Documentation for this workflow can be found here.
This workflow is part of Biowdl developed by the SASC team at Leiden University Medical Center.
For any question related to germline-DNA, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.