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@gatk-workflows GATK workflows

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    29 repositories

    • gatk4-data-processing

      Public
      Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •78•158•5•2•Updated Aug 10, 2022Aug 10, 2022

    • gatk4-rnaseq-germline-snps-indels

      Public
      Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •37•81•0•2•Updated Sep 13, 2021Sep 13, 2021

    • seq-format-conversion

      Public
      Workflows for converting between sequence data formats
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •30•39•0•1•Updated Sep 5, 2021Sep 5, 2021

    • utility-wdls

      Public
      Short workflows to run common tasks.
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated May 12, 2021May 12, 2021

    • gatk4-germline-snps-indels

      Public
      Workflows for germline short variant discovery with GATK4
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •55•138•2•0•Updated May 7, 2021May 7, 2021

    • gatk4-genome-processing-pipeline

      Public archive
      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 This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.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 "New" or "Revised" License
      •41•28•0•2•Updated Jan 4, 2021Jan 4, 2021

    • gatk4-basic-variant-validation

      Public
      Simple workflow to validate a VCF (or GVCF)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 4, 2020Nov 4, 2020

    • seq-format-validation

      Public
      Workflows for validating sequence data formats
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •4•2•0•0•Updated Nov 4, 2020Nov 4, 2020

    • gatk4-exome-analysis-pipeline

      Public archive
      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 "New" or "Revised" License
      •42•55•0•0•Updated Oct 29, 2020Oct 29, 2020

    • gatk4-basic-joint-genotyping

      Public
      Basic joint genotyping with GATK4. NOT Best Practices, only for teaching/demo purposes.
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •0•6•1•0•Updated Oct 11, 2020Oct 11, 2020

    • intel-gatk4-germline-snps-indels

      Public
      Workflows for germline short variant discovery with GATK4 optimized by Intel for on-premises infrastructure
      WDL
      •4•4•0•0•Updated Aug 10, 2020Aug 10, 2020

    • broad-prod-wgs-germline-snps-indels

      Public
      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 "New" or "Revised" License
      •26•56•0•1•Updated Mar 19, 2020Mar 19, 2020

    • gatk4-germline-cnvs

      Public archive
      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•2•1•1•Updated Mar 18, 2020Mar 18, 2020

    • gatk4-somatic-cnvs

      Public archive
      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 "New" or "Revised" License
      •20•44•4•1•Updated Mar 10, 2020Mar 10, 2020

    • generic-wdl-script

      Public archive
      This generic wdl script will be for users seeking to quickly run a shell command
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•0•0•Updated Mar 9, 2020Mar 9, 2020

    • gatk4-somatic-snvs-indels

      Public archive
      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.
      tumorgatkvariantsmutect
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •42•77•4•0•Updated Mar 9, 2020Mar 9, 2020

    • gatk4-pathseq

      Public archive
      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 "New" or "Revised" License
      •5•10•1•0•Updated Mar 9, 2020Mar 9, 2020

    • gatk4-mitochondria-pipeline

      Public archive
      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 "New" or "Revised" License
      •9•22•1•0•Updated Mar 9, 2020Mar 9, 2020

    • gatk4-cnn-variant-filter

      Public archive
      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 "New" or "Revised" License
      •15•8•0•0•Updated Mar 5, 2020Mar 5, 2020

    • five-dollar-genome-analysis-pipeline

      Public archive
      Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •43•57•4•0•Updated Jan 24, 2020Jan 24, 2020

    • gatk4-jupyter-notebook-tutorials

      Public
      This repository contains Jupyter Notebooks containing GATK Best Practices Workflows
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •13•26•0•0•Updated Dec 19, 2019Dec 19, 2019

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

      Public archive
      Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •24•54•3•0•Updated Dec 19, 2019Dec 19, 2019

    • gatk4-somatic-with-preprocessing

      Public
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •2•6•2•0•Updated Dec 19, 2019Dec 19, 2019

    • gatk3-germline-snps-indels

      Public
      Workflows for germline short variant discovery with GATK3
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Aug 9, 2019Aug 9, 2019

    • gatk3-data-processing

      Public
      Workflows for processing high-throughput sequencing data for variant discovery with GATK3 and related tools
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•2•Updated Aug 9, 2019Aug 9, 2019

    • intel-faster-alternative-samples

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

    • intel-gatk4-somatic-with-preprocessing

      Public
      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 "New" or "Revised" License
      •3•6•0•0•Updated May 16, 2018May 16, 2018

    • intel-gatk3-4-germline-snps-indels

      Public
      Workflows for processing and variant discovery with GATK (v3+v4) optimized by Intel for on-premises infrastructure
      WDL
      •4•6•0•0•Updated Mar 15, 2018Mar 15, 2018

    • intel-gatk3-germline-snps-indels

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