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@gatk-workflows

GATK workflows

Official GATK workflows published by the Broad Institute's Data Sciences Platform

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  1. gatk4-germline-snps-indels gatk4-germline-snps-indels Public

    Workflows for germline short variant discovery with GATK4

    WDL 133 56

  2. gatk4-data-processing gatk4-data-processing Public

    Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

    WDL 149 75

  3. gatk4-rnaseq-germline-snps-indels gatk4-rnaseq-germline-snps-indels Public

    Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

    WDL 72 37

  4. seq-format-conversion seq-format-conversion Public

    Workflows for converting between sequence data formats

    WDL 37 29

  5. seq-format-validation seq-format-validation Public

    Workflows for validating sequence data formats

    WDL 2 4

  6. gatk4-basic-joint-genotyping gatk4-basic-joint-genotyping Public

    Basic joint genotyping with GATK4. NOT Best Practices, only for teaching/demo purposes.

    WDL 6 1

Repositories

Showing 10 of 29 repositories
  • gatk4-data-processing Public

    Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

    gatk-workflows/gatk4-data-processing’s past year of commit activity
    WDL 149 BSD-3-Clause 75 5 2 Updated Aug 10, 2022
  • gatk4-rnaseq-germline-snps-indels Public

    Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

    gatk-workflows/gatk4-rnaseq-germline-snps-indels’s past year of commit activity
    WDL 72 BSD-3-Clause 37 0 2 Updated Sep 13, 2021
  • seq-format-conversion Public

    Workflows for converting between sequence data formats

    gatk-workflows/seq-format-conversion’s past year of commit activity
    WDL 37 BSD-3-Clause 29 0 1 Updated Sep 5, 2021
  • utility-wdls Public

    Short workflows to run common tasks.

    gatk-workflows/utility-wdls’s past year of commit activity
    WDL 2 BSD-3-Clause 0 0 0 Updated May 12, 2021
  • gatk4-germline-snps-indels Public

    Workflows for germline short variant discovery with GATK4

    gatk-workflows/gatk4-germline-snps-indels’s past year of commit activity
    WDL 133 BSD-3-Clause 56 2 0 Updated May 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.

    gatk-workflows/gatk4-genome-processing-pipeline’s past year of commit activity
    WDL 26 BSD-3-Clause 43 0 2 Updated Jan 4, 2021
  • gatk4-basic-variant-validation Public

    Simple workflow to validate a VCF (or GVCF)

    gatk-workflows/gatk4-basic-variant-validation’s past year of commit activity
    WDL 0 BSD-3-Clause 0 0 0 Updated Nov 4, 2020
  • seq-format-validation Public

    Workflows for validating sequence data formats

    gatk-workflows/seq-format-validation’s past year of commit activity
    WDL 2 BSD-3-Clause 4 0 0 Updated Nov 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.

    gatk-workflows/gatk4-exome-analysis-pipeline’s past year of commit activity
    WDL 50 BSD-3-Clause 41 0 0 Updated Oct 29, 2020
  • gatk4-basic-joint-genotyping Public

    Basic joint genotyping with GATK4. NOT Best Practices, only for teaching/demo purposes.

    gatk-workflows/gatk4-basic-joint-genotyping’s past year of commit activity
    WDL 6 BSD-3-Clause 1 1 0 Updated Oct 11, 2020
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