Story #15996

Updated by Peter Amstutz 6 months 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.

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 minimal automated interpretation (CLINVAR annotation with SnpEff?) interpretation.

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