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Idea #15996

Updated by Peter Amstutz almost 5 years ago

Find community-built best practices GATK4 variant calling CWL and/or create one from scratch 

 Run on several PGP samples using su92l 

 Put everything in a public project and document it thoroughly. 

 Do some reporting (Multi-QC) and automated interpretation (CLINVAR annotation with SnpEff?) 

 Stretch goals: 

 Second pipeline using Deep Variant 

 gVCF output is suitable to feed directly into the Lightning CWL for tiling. 

 Do some reporting (Multi-QC) and automated interpretation (CLINVAR annotation with SnpEff?)

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