User: vdauwera

gravatar for vdauwera
vdauwera890
Reputation:
890
Status:
Trusted
Location:
Cambridge, MA
Website:
http://www.broadinstit...
Last seen:
2 days, 6 hours ago
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

<prev • 50 results • page 1 of 5 • next >
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Answer: A: GATK best practices for Broad-produced NGS data
... 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 vdauwera890
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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 ...
written 5 days ago by vdauwera890 • updated 5 days ago by genomax59k
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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 6 months ago by vdauwera890
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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 7 months ago by vdauwera890
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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 7 months ago by vdauwera890
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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 8 months ago by vdauwera890
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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 8 months ago by vdauwera890
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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 vdauwera890
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Answer: A: Realignment disappeared in gatk4
... Also https://software.broadinstitute.org/gatk/blog?id=7847 ...
written 8 months ago by vdauwera890
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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 8 months ago by vdauwera890

Latest awards to vdauwera

Appreciated 5 days ago, created a post with more than 5 votes. For A: Variant Calls: Freebayes vs GATK
Scholar 5 days ago, created an answer that has been accepted. For A: GATK Workflow for GATK in Cancer Samples
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Appreciated 6 months ago, created a post with more than 5 votes. For A: Variant Calls: Freebayes vs GATK
Popular Question 6 months ago, created a question with more than 1,000 views. For Gatk Workshop Survey
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Scholar 8 months ago, created an answer that has been accepted. For A: GATK Workflow for GATK in Cancer Samples
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Popular Question 11 months ago, created a question with more than 1,000 views. For Scientific Technical Writer -- Help us write papers about GATK!
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Scientific Technical Writer -- Help us write papers about GATK!
Popular Question 3.5 years ago, created a question with more than 1,000 views. For The Gatk Has A New Website And Forum!
Scholar 3.5 years ago, created an answer that has been accepted. For A: GATK Workflow for GATK in Cancer Samples
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Appreciated 4.0 years ago, created a post with more than 5 votes. For Scientific Technical Writer -- Help us write papers about GATK!
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Scientific Technical Writer -- Help us write papers about GATK!
Appreciated 4.7 years ago, created a post with more than 5 votes. For The Gatk Has A New Website And Forum!
Appreciated 5.0 years ago, created a post with more than 5 votes. For The Gatk Has A New Website And Forum!
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