User: vdauwera
vdauwera • 890
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- Location:
- Cambridge, MA
- Website:
- http://www.broadinstit...
- Last seen:
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- Joined:
- 6 years, 7 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
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... It depends what form of the data you’re starting from. If you’re starting from true raw WGS data, ie unmapped reads (in fastq or ubam) then you should follow the best practices as laid out in the GATK documentation. However if you’re starting from an aligned bam or cram file you received from the Br ...
written 2 days ago by
vdauwera • 890
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Answer:
A: Bash vs WDL for running GATK
... WDL is intended to help you automate the work by chaining together commands, so you don't have to do it manually. The result is called a workflow or pipeline. There are other languages and systems besides WDL that allow you to do this. The main advantage of WDL is that it is what the GATK team uses ...
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... 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 6 months ago by
vdauwera • 890
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... 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 7 months ago by
vdauwera • 890
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... 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 7 months ago by
vdauwera • 890
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... 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 8 months ago by
vdauwera • 890
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... 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 8 months ago by
vdauwera • 890
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Answer:
A: GATK4 training for beginners
... Also, for training events, see https://software.broadinstitute.org/gatk/events/ ...
written 8 months ago by
vdauwera • 890
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... Also https://software.broadinstitute.org/gatk/blog?id=7847 ...
written 8 months ago by
vdauwera • 890
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... 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 8 months ago by
vdauwera • 890
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