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Geraldine Van der Auwera

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Latest activity by Geraldine Van der Auwera
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    Geraldine Van der Auwera commented,

    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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    Geraldine Van der Auwera commented,

    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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    Geraldine Van der Auwera commented,

    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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    Geraldine Van der Auwera commented,

    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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    Geraldine Van der Auwera commented,

    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-...

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    Geraldine Van der Auwera commented,

    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...

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    Geraldine Van der Auwera created an article,

    New Year update — GATK takes on 2021

    Well folks, this new year is off to a heck of a start. I don't know who needs to hear this but it's okay to be struggling. On our end, we're going to do whatever we can to support your work, so don...

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    Geraldine Van der Auwera commented,

    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.

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    Geraldine Van der Auwera created an article,

    DRAGEN-GATK update: Upcoming webinar and pipeline release timeframe

    A year ago this month, we announced the start of our collaboration with the DRAGEN team at Illumina, which aims to combine the respective strengths of GATK and DRAGEN as well as promote the standar...

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    Geraldine Van der Auwera commented,

    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 ...