Geraldine Van der Auwera
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Votes on activity by Geraldine Van der Auwera Sort by votes-
MICHAEL MCMANUS Mutect2 and the somatic short variants pipeline are on the list of use cases we want to work on together, but we haven't yet decided which will be next after the germline short vari...
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Got it — that should not make any difference. The only case where things could get weird is if you're splitting up chromosomes internally, because then you could run into edge effects. But if you'r...
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Oh yes I didn't mention processing only intervals since you already mentioned doing that, but it is definitely key. I'm not entirely sure I understand what you mean by "using only the "relevant" FA...
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Ah I see. Unfortunately we don't yet have systematic documentation on the pipeline optimizations, but off the top of my head, the top three are (1) using preemptible VMs on GCP (analogous to Spot i...
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Hi Ury Alon, the next pipeline/use case we are tackling as part of the DRAGEN-GATK collaboration is germline SV (structural variation), which is a big area of focus for us right now. We don't curre...
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FYI our colleagues in the Genomics Platform (who do the sequencing at the Broad Institute) are presenting a poster at the AGBT meeting this week about their testing of the DRAGEN-GATK pipeline. For...
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Thanks ajwils, we'll do our best not to let you all down. I asked about the editor, unfortunately that's a limitation of Zendesk. Apparently there's an upgrade coming so we'll see what that provid...
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Ah I see what you mean, thanks for clarifying. To be frank, we considered doing that but decided to take a different approach in order to boost the sustainability of our knowledge base. Part of why...
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You will need to ask your question again in the new forum. Sorry about that -- I forgot to include that point in my post. If you let them know that it's a repost from the old forum (eg add "Repost:...
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Official comment The GATK resource bundle is not subject to any use restrictions (so it's ok to use it for commercial purposes).