7 open source projects by gatk-workflows

This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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.

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

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 PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline

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.

Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools

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 This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.

Workflows for germline short variant discovery with GATK4