GATK4 automated pipelines in existence?

This page summarizes the projects mentioned and recommended in the original post on /r/bioinformatics
nextflow Workflow Pipeline Bioinformatics Genomics

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  • GATK

    Germline Variant Calling Nextflow Pipeline Based On GATK4 Best Practices

    • Are you looking for a germline variant calling pipeline? If so, try https://github.com/lifebit-ai/GATK. If you know Nextflow, you can edit the script. Apparently, it uses Docker so you get the containerization.

  • sarek

    Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

    • The sarek pipeline from nf-core might interest you

  • InfluxDB

    Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

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NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a more popular project.

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