gatk-prepocess

This Biowdl workflow will preprocess a BAM file, preparing it for variantcalling based on the GATK Best Practises.

Documentation

You can find the documentation here.

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

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

Name	Name	Last commit message	Last commit date
Latest commit rhpvorderman Merge pull request #45 from biowdl/BIOWDL-538_2 Feb 15, 2022 1bdf81e · Feb 15, 2022 History 306 Commits
.github	.github	Use ci_tests file	Feb 15, 2022
docs	docs	fix formatting index.md	Aug 5, 2020
scripts @ 84690a3	scripts @ 84690a3	update submodules	Jul 15, 2021
tasks @ 3a01f3b	tasks @ 3a01f3b	update submodules	Jul 15, 2021
tests	tests	Scatters should be given externally	Jun 10, 2020
.gitmodules	.gitmodules	add scripts submodule	Feb 25, 2019
CHANGELOG.md	CHANGELOG.md	set to stable verion	Aug 5, 2020
LICENSE	LICENSE	change license header appropriately	Feb 21, 2019
README.md	README.md	fix whitespace	Aug 14, 2019
VERSION	VERSION	setting next version	Jul 15, 2021
ci_tests.json	ci_tests.json	Use ci_tests file	Feb 15, 2022
gatk-preprocess.wdl	gatk-preprocess.wdl	set splitncigar to old estimate	Jul 29, 2020
requirements-test.txt	requirements-test.txt	Fix my dumb mistake.	Dec 11, 2020