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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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validation 2020 #3038

Closed naumenko-sa closed 4 years ago

naumenko-sa commented 4 years ago

Hello!

Starting this thread to update variant calling validation in bcbio.

Users reported some validation results, based on NA12878 and another 6 NA12XXXXX samples, showing that gatk4.1 + bcbio filters result in somewhat lower indel calling precision: 90% vs 95% compared to another GATK workflows.

SErgey

roryk commented 4 years ago

Great-- do we have links to the results? It would be good to see where we might be missing stuff.

naumenko-sa commented 4 years ago

closing for now, goes to circle 3