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Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
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Workflows for germline short variant discovery with GATK4
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Workflows for somatic short variant discovery with GATK4
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Workflows used in production at Broad for germline short variant discovery in WGS data
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Workflows used for germline short variant discovery in WGS data
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Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools
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Secondary analysis pipelines
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Workflows for somatic copy number variant discovery with GATK4
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Pipeline for structural variation detection in cohorts
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a place for topmed workflows
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Workflows for converting between sequence data formats
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A collection of reusable WDL tasks. Category:Other
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bioinformatics pipelines
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WDL workflow for population variant calling using htsget, DeepVariant, and GLnexus
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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.
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Workflow Description Language (WDL) scripts for common vg workflows
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WDL / Cromwell Sandbox
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Miscellaneous workflows optimized by Intel to be fast-running
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HiC uniform processing pipeline
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Workflows for processing and variant discovery with GATK (v3+v4) optimized by Intel for on-premises infrastructure
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Klarman Cell Observatory tools, workflows, and spells
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Improving deep learning variant calling methods for BGI-SEQ
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development location for a wdl based germline pipeline with scatter gather parallelization
