GATK workflows

gatk4-data-processing Public

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

WDL 163BSD-3-Clause 78 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

WDL 86BSD-3-Clause 37 0 2 Updated Sep 13, 2021

seq-format-conversion Public

Workflows for converting between sequence data formats

WDL 40BSD-3-Clause 32 0 1 Updated Sep 5, 2021

utility-wdls Public

Short workflows to run common tasks.

WDL 2BSD-3-Clause 0 0 0 Updated May 12, 2021

gatk4-germline-snps-indels Public

Workflows for germline short variant discovery with GATK4

WDL 145BSD-3-Clause 54 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 This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.

WDL 28BSD-3-Clause 40 0 2 Updated Jan 4, 2021

gatk4-basic-variant-validation Public

Simple workflow to validate a VCF (or GVCF)

WDL 0BSD-3-Clause 0 0 0 Updated Nov 4, 2020

seq-format-validation Public

Workflows for validating sequence data formats

WDL 2BSD-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.

WDL 56BSD-3-Clause 42 0 0 Updated Oct 29, 2020

gatk4-basic-joint-genotyping Public

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

WDL 7BSD-3-Clause 0 1 0 Updated Oct 11, 2020

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