GATK workflows

Repositories

• seq-format-conversion

  Workflows for converting between sequence data formats
  wdl BSD-3-Clause 17 15 0 0 Updated Jan 7, 2021

• gatk4-genome-processing-pipeline Archived

  Workflows used for processing whole genome sequence data + germline variant calling. This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.
  wdl BSD-3-Clause 25 16 0 2 Updated Jan 4, 2021

• gatk4-germline-snps-indels

  Workflows for germline short variant discovery with GATK4
  wdl BSD-3-Clause 47 86 2 0 Updated Nov 24, 2020

• gatk4-rnaseq-germline-snps-indels

  Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
  wdl BSD-3-Clause 9 14 0 0 Updated Nov 18, 2020

• utility-wdls

  Short workflows to run common tasks.
  wdl BSD-3-Clause 0 0 0 0 Updated Nov 9, 2020

• gatk4-basic-variant-validation

  Simple workflow to validate a VCF (or GVCF)
  wdl BSD-3-Clause 0 0 0 0 Updated Nov 4, 2020

• seq-format-validation

  Workflows for validating sequence data formats
  wdl BSD-3-Clause 3 1 0 0 Updated Nov 4, 2020

• gatk4-exome-analysis-pipeline Archived

  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.
  wdl BSD-3-Clause 34 37 0 0 Updated Oct 29, 2020

• gatk4-data-processing

  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  wdl BSD-3-Clause 59 84 5 0 Updated Oct 16, 2020

• gatk4-basic-joint-genotyping

  Basic joint genotyping with GATK4. NOT Best Practices, only for teaching/demo purposes.
  wdl BSD-3-Clause 0 2 0 0 Updated Oct 11, 2020

• intel-gatk4-germline-snps-indels

  Workflows for germline short variant discovery with GATK4 optimized by Intel for on-premises infrastructure
  wdl 5 2 0 0 Updated Aug 10, 2020

• broad-prod-wgs-germline-snps-indels

  Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline
  wdl BSD-3-Clause 27 40 0 1 Updated Mar 19, 2020

• gatk4-germline-cnvs Archived

  This repo will be archived soon, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
  3 1 1 1 Updated Mar 18, 2020

• gatk4-somatic-cnvs Archived

  This repo is archived, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
  wdl BSD-3-Clause 19 31 4 1 Updated Mar 10, 2020

• generic-wdl-script Archived

  This generic wdl script will be for users seeking to quickly run a shell command
  wdl BSD-3-Clause 2 1 0 0 Updated Mar 9, 2020

• gatk4-somatic-snvs-indels Archived

  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

  tumor gatk variants mutect
  wdl BSD-3-Clause 36 59 4 0 Updated Mar 9, 2020

• gatk4-pathseq Archived

  This repo is archived, the these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
  wdl BSD-3-Clause 2 3 1 0 Updated Mar 9, 2020

• gatk4-mitochondria-pipeline Archived

  This repo is be archived, these workflows are still housed housed in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
  wdl BSD-3-Clause 4 11 1 0 Updated Mar 9, 2020

• gatk4-cnn-variant-filter Archived

  This repo is archived, the these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
  wdl BSD-3-Clause 12 5 0 0 Updated Mar 5, 2020

• five-dollar-genome-analysis-pipeline Archived

  Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline
  wdl BSD-3-Clause 33 43 4 0 Updated Jan 24, 2020

• gatk4-jupyter-notebook-tutorials

  This repository contains Jupyter Notebooks containing GATK Best Practices Workflows
  Jupyter Notebook BSD-3-Clause 8 8 0 0 Updated Dec 20, 2019

• gatk3-4-rnaseq-germline-snps-indels Archived

  Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools
  wdl BSD-3-Clause 19 35 3 0 Updated Dec 19, 2019

• gatk4-somatic-with-preprocessing
  wdl BSD-3-Clause 2 3 2 0 Updated Dec 19, 2019

• gatk3-germline-snps-indels

  Workflows for germline short variant discovery with GATK3
  wdl BSD-3-Clause 2 0 0 0 Updated Aug 9, 2019

• gatk3-data-processing

  Workflows for processing high-throughput sequencing data for variant discovery with GATK3 and related tools
  wdl BSD-3-Clause 1 0 0 2 Updated Aug 9, 2019

• intel-faster-alternative-samples

  Miscellaneous workflows optimized by Intel to be fast-running
  wdl 0 3 0 0 Updated Jul 23, 2018

• intel-gatk4-somatic-with-preprocessing

  Workflows for data pre-processing and initial calling of somatic SNP, Indel, and copy number variants optimized by Intel for on-premises infrastructure
  wdl BSD-3-Clause 4 3 0 0 Updated May 16, 2018

• intel-gatk3-4-germline-snps-indels

  Workflows for processing and variant discovery with GATK (v3+v4) optimized by Intel for on-premises infrastructure
  wdl 4 3 0 0 Updated Mar 15, 2018

• intel-gatk3-germline-snps-indels

  Workflows for processing and variant discovery with GATK optimized by Intel for on-premises infrastructure
  wdl 0 0 0 0 Updated Nov 9, 2017