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All Projects → biowdl → germline-DNA

biowdl / germline-DNA

Licence: MIT License
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

Programming Languages

wdl
31 projects
python
139335 projects - #7 most used programming language

Labels

pipelinevariantcallingmultisamplegatk4gatk-bestpractices

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germline-DNA

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

Documentation for this workflow can be found here.

About

This workflow is part of Biowdl developed by the SASC team at Leiden University Medical Center.

Contact

For any question related to germline-DNA, please use the github issue tracker or contact the SASC team directly at: [email protected].

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