User: vdauwera

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vdauwera920
Reputation:
920
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Trusted
Location:
Cambridge, MA
Website:
http://www.broadinstit...
Last seen:
1 month, 2 weeks ago
Joined:
7 years, 2 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 • 51 results • page 1 of 6 • next >
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Comment: C: How Much Does It Cost To Align A Flowcell In The Cloud?
... Nope that’s the cost for anyone who uses our pipeline on Google, for a single whole genome, going from unmapped reads to GVCF or VCF, including QC. Nothing to do with scale or pref pricing, except that we benefitted from GCP engineers’ help to optimize the pipeline. Check it out [here][1] [1]: ht ...
written 7 weeks ago by vdauwera920 • updated 6 weeks ago by RamRS22k
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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 6 months ago by vdauwera920
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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 6 months ago by vdauwera920 • updated 6 months ago by genomax68k
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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 12 months ago by vdauwera920
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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 13 months ago by vdauwera920
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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 14 months ago by vdauwera920
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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 14 months ago by vdauwera920
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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 15 months ago by vdauwera920
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Answer: A: GATK4 training for beginners
... Also, for training events, see https://software.broadinstitute.org/gatk/events/ ...
written 15 months ago by vdauwera920
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Answer: A: Realignment disappeared in gatk4
... Also https://software.broadinstitute.org/gatk/blog?id=7847 ...
written 15 months ago by vdauwera920

Latest awards to vdauwera

Teacher 6 months 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
Scholar 6 months ago, created an answer that has been accepted. For A: GATK Workflow for GATK in Cancer Samples
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Appreciated 12 months ago, created a post with more than 5 votes. For A: Variant Calls: Freebayes vs GATK
Popular Question 12 months ago, created a question with more than 1,000 views. For Gatk Workshop Survey
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Scholar 15 months ago, created an answer that has been accepted. For A: GATK Workflow for GATK in Cancer Samples
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Popular Question 18 months ago, created a question with more than 1,000 views. For Scientific Technical Writer -- Help us write papers about GATK!
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Scientific Technical Writer -- Help us write papers about GATK!
Popular Question 4.0 years ago, created a question with more than 1,000 views. For The Gatk Has A New Website And Forum!
Scholar 4.0 years ago, created an answer that has been accepted. For A: GATK Workflow for GATK in Cancer Samples
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: GATK Workflow for GATK in Cancer Samples
Appreciated 4.5 years ago, created a post with more than 5 votes. For Scientific Technical Writer -- Help us write papers about GATK!
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Scientific Technical Writer -- Help us write papers about GATK!
Appreciated 5.2 years ago, created a post with more than 5 votes. For The Gatk Has A New Website And Forum!
Appreciated 5.5 years ago, created a post with more than 5 votes. For The Gatk Has A New Website And Forum!
Autobiographer 5.5 years ago, has more than 80 characters in the information field of the user's profile.

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