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Diff for: docs/GATK_GERMLINE_README.md

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Kids First Data Resource Center Single Sample Genotyping Workflow. This workflow closely mirrors the [Kids First DRC Joint Genotyping Workflow](https://github.com/kids-first/kf-jointgenotyping-workflow/blob/master/workflow/kfdrc_jointgenotyping_refinement_workflow.cwl).
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While the Joint Genotyping Workflow is meant to be used with trios, this workflow is meant for processing single samples.
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The key difference in this pipeline is a change in filtering between when the final VCF is gathered by GATK GatherVcfCloud and when it is annotated by VEP.
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Unlike the Joint Genotyping Workflow, a germline-oriented [GATK hard filtering process](https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants) is performed and no CalculateGenotypePosteriors has been removed.
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Unlike the Joint Genotyping Workflow, a germline-oriented [GATK hard filtering process](https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants) is performed and CalculateGenotypePosteriors has been removed.
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While somatic samples can be run through this workflow, be wary that the filtering process is specifically tuned for germline data.
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If you would like to run this workflow using the cavatica public app, a basic primer on running public apps can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-Cavatica-af5ebb78c38a4f3190e32e67b4ce12bb).

Diff for: workflows/kfdrc-single-sample-genotyping-wf.cwl

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Kids First Data Resource Center Single Sample Genotyping Workflow. This workflow closely mirrors the [Kids First DRC Joint Genotyping Workflow](https://github.com/kids-first/kf-jointgenotyping-workflow/blob/master/workflow/kfdrc_jointgenotyping_refinement_workflow.cwl).
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While the Joint Genotyping Workflow is meant to be used with trios, this workflow is meant for processing single samples.
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The key difference in this pipeline is a change in filtering between when the final VCF is gathered by GATK GatherVcfCloud and when it is annotated by VEP.
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Unlike the Joint Genotyping Workflow, a germline-oriented [GATK hard filtering process](https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants) is performed and no CalculateGenotypePosteriors has been removed.
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Unlike the Joint Genotyping Workflow, a germline-oriented [GATK hard filtering process](https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants) is performed and CalculateGenotypePosteriors has been removed.
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While somatic samples can be run through this workflow, be wary that the filtering process is specifically tuned for germline data.
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If you would like to run this workflow using the cavatica public app, a basic primer on running public apps can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-Cavatica-af5ebb78c38a4f3190e32e67b4ce12bb).

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