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  1. broadinstitute/gatk broadinstitute/gatk Public

    Official code repository for GATK versions 4 and up

    Java 1.7k 594

  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 986 369

  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 359

  4. openwdl/wdl openwdl/wdl Public

    Workflow Description Language - Specification and Implementations

    780 306

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    This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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