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broadinstitute/gatk
broadinstitute/gatk PublicOfficial code repository for GATK versions 4 and up
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broadinstitute/picard
broadinstitute/picard PublicA set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
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broadinstitute/cromwell
broadinstitute/cromwell PublicScientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
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openwdl/wdl
openwdl/wdl PublicWorkflow Description Language - Specification and Implementations
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gatk-workflows/gatk4-germline-snps-indels
gatk-workflows/gatk4-germline-snps-indels PublicWorkflows for germline short variant discovery with GATK4
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gatk-workflows/gatk4-somatic-snvs-indels
gatk-workflows/gatk4-somatic-snvs-indels Public archiveThis repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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…
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