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1. broadinstitute/gatk broadinstitute/gatk Public

   Official code repository for GATK versions 4 and up

   Java 1.7k 590

2. broadinstitute/picard broadinstitute/picard Public

   A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

   Java 983 368

3. broadinstitute/cromwell broadinstitute/cromwell Public

   Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

   Scala 995 360

4. openwdl/wdl openwdl/wdl Public

   Workflow Description Language - Specification and Implementations

   772 307

5. gatk-workflows/gatk4-germline-snps-indels gatk-workflows/gatk4-germline-snps-indels Public

   Workflows for germline short variant discovery with GATK4

   WDL 133 56

6. gatk-workflows/gatk4-somatic-snvs-indels gatk-workflows/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   This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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 Workflo…

   WDL 76 44