sripaladugu / gatk-variantcalling Public

forked from biowdl/gatk-variantcalling

Notifications You must be signed in to change notification settings
Fork 0
Star 0

A pipeline that calls variants on a group of BAM files. Category:Multi-Sample

biowdl.github.io/gatk-variantcalling

MIT license

0 stars 3 forks Branches Tags Activity

Star

Notifications

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 291 Commits
.github		.github
docs		docs
scripts @ c0b48b0		scripts @ c0b48b0
tasks @ d1e2d6e		tasks @ d1e2d6e
tests		tests
.gitmodules		.gitmodules
.travis.yml		.travis.yml
CHANGELOG.md		CHANGELOG.md
LICENSE		LICENSE
README.md		README.md
VERSION		VERSION
calculate-regions.wdl		calculate-regions.wdl
dockerImages.yml		dockerImages.yml
docker_slurm.conf		docker_slurm.conf
gatk-variantcalling.options.json		gatk-variantcalling.options.json
jointgenotyping.wdl		jointgenotyping.wdl
multisample-variantcalling.wdl		multisample-variantcalling.wdl
requirements-test.txt		requirements-test.txt
single-sample-variantcalling.wdl		single-sample-variantcalling.wdl

Repository files navigation

Gatk-variantcalling

This repository contains a Biowdl workflows which uses Haplotypecaller to perform variantcalling.

Documentation

You can find the documentation here

About

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

Usage

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