User: vdauwera

gravatar for vdauwera
vdauwera800
Reputation:
800
Status:
Trusted
Location:
Cambridge, MA
Website:
http://www.broadinstit...
Last seen:
2 months, 2 weeks ago
Joined:
6 years, 4 months ago
Email:
v*******@broadinstitute.org

Associate Director of Outreach and Communications for the Data Sciences Platform at the Broad Institute in Cambridge, MA. I'm responsible for keeping the research community that uses DSP software happy and well-informed about our tools and how to use them. Our software products include GATK, Picard, Cromwell/WDL and FireCloud.

Posts by vdauwera

<prev • 48 results • page 1 of 5 • next >
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Answer: A: Can someone please help me run any GATK4 pipeline?
... Hey everyone, this is a bit of a rabbit hole, let's take a step back. If you're going to be running the pipelines on a platform other than Google Cloud you need to use a (slightly) different pipeline script (for computational efficiency) and manage data access differently. I can follow up here: http ...
written 11 weeks ago by vdauwera800
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Answer: A: GATK4 local computing workflow
... Assuming you're talking about the germline short variants discovery pipeline, we have several different versions; aside from the cloud-optimized pipeline we also have one that is optimized for local execution. They are summarized here: https://software.broadinstitute.org/gatk/best-practices/workflow ...
written 3 months ago by vdauwera800
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Answer: A: Strategy in WGS variant calling using GATK (CombineGVCF step)
... A simpler way of using a list of contigs or intervals to restrict analysis to areas of interest is to provide the list through the `-L` argument at the HaplotypeCaller stage (which will also take a lot less time to run). If you already have generated GVCFs then you can instead use the list of interv ...
written 3 months ago by vdauwera800
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Comment: A: InDel marker using GATK and Mummer
... If you explain in more detail what you did (including commands) on the GATK forum we can try to help you. https://gatkforums.broadinstitute.org/gatk ...
written 4 months ago by vdauwera800
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Answer: A: Variant Calls: Freebayes vs GATK
... Keep in mind that the GATK variant callers are designed to be as sensitive as possible and will therefore include many false positives, so you need to apply some filtering steps after calling to remove those false positives, as described in the GATK Best Practices. It's essentially impossible to ans ...
written 4 months ago by vdauwera800
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Answer: A: GATK4 training for beginners
... Also, for training events, see https://software.broadinstitute.org/gatk/events/ ...
written 4 months ago by vdauwera800
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Answer: A: Realignment disappeared in gatk4
... Also https://software.broadinstitute.org/gatk/blog?id=7847 ...
written 4 months ago by vdauwera800
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Comment: C: GATK: Unzipped files Cannot Find GenomeAnalysisTK.jar?
... Please use the gatk wrapper script rather than calling the jars directly. See the docs for an explanation of why. Follow the quick start guide here: https://software.broadinstitute.org/gatk/documentation/quickstart ...
written 5 months ago by vdauwera800
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News: Deep learning in GATK4
... Sam Friedman, deep learning developer on the GATK4 team, wrote a blog post about his work, which people interested in genomic applications of deep learning may find of interest: https://software.broadinstitute.org/gatk/blog?id=10996 ...
gatk4 gatk news deep learning written 7 months ago by vdauwera800
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News: Free credits for running GATK4 pipelines in the cloud
... As announced on the GATK blog: > With the GATK4 release just around the corner, we wanted to make it > easy for everyone to try out the new pipelines without going through a > whole lot of setup. So we're setting them all up in ready-to-run > workspaces on FireCloud, which is a secure, ...
gatk4 gatk news cloud written 7 months ago by vdauwera800

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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Scholar 4 months ago, created an answer that has been accepted. For A: GATK Workflow for GATK in Cancer Samples
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Popular Question 7 months ago, created a question with more than 1,000 views. For Scientific Technical Writer -- Help us write papers about GATK!
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Scientific Technical Writer -- Help us write papers about GATK!
Popular Question 3.1 years ago, created a question with more than 1,000 views. For The Gatk Has A New Website And Forum!
Scholar 3.1 years ago, created an answer that has been accepted. For A: GATK Workflow for GATK in Cancer Samples
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
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