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1. broadinstitute/gatk broadinstitute/gatk Public

   Official code repository for GATK versions 4 and up

   Java 1.8k 603

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 1k 373

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 1k 361

4. openwdl/wdl openwdl/wdl Public

   Specification for the Workflow Description Language (WDL).

   808 308

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

   Workflows for germline short variant discovery with GATK4

   WDL 134 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   This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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 77 43