Geraldine Van der Auwera
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The GATK resource bundle is not subject to any use restrictions (so it's ok to use it for commercial purposes).
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...
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...
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...
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...
Hi Marsha Wallace, Matthias De Smet, Karynne Patterson, Apologies for the delay -- we posted an update on the blog last week, see https://gatk.broadinstitute.org/hc/en-us/articles/360055062832-New-...
Hi Ana Rita Marques, Yes we dropped the indel realignment step from the Best Practices; I think that was about 2 years ago. There was a blog post about it. We found that this step was no longer use...
Hi Matthew Porter, we don't have any plans to make anything specific for ARM at this time. It's all open source though so you're welcome to do so yourself.
Hi Niko Balanis, glad to hear you're enjoying that blazing speed :) Let me loop in Bhanu Gandham to find out if we have the evaluation parameters in a shareable format. I'm pretty sure it's in the ...
Hi Dr. venkateswara swamy, the syntax has changed in GATK 4 so you cannot use scripts written for earlier versions without modification. For example, this error is pointing out that the “-T” argume...