User: vdauwera
vdauwera • 990
- Reputation:
- 990
- Status:
- Trusted
- Location:
- Cambridge, MA
- Website:
- https://broadinstitute...
- Twitter:
- VdaGeraldine
- Last seen:
- 2 weeks, 2 days ago
- Joined:
- 8 years, 9 months ago
- Email:
- v*******@broadinstitute.org
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, Cromwell, and Terra.bio, and we are involved in the development of Picard and the WDL workflow language.
Posts by vdauwera
<prev
• 59 results •
page 1 of 6 •
next >
0
votes
1
answer
137
views
1
answers
... BQSR is still recommended in the current pipelines but will be retired when the DRAGEN-GATK pipeline comes out later this quarter. ...
written 23 days ago by
vdauwera • 990
2
votes
1
answer
137
views
1
answers
... If I recall correctly the BGI sequencing technology is close enough to Illumina's that you can use ILLUMINA as PL for BQSR. The PL is just a check to catch certain sequencing types that are so different that the data can't be processed through BQSR. ...
written 23 days ago by
vdauwera • 990
1
vote
0
answers
249
views
0
answers
... Hi all, I just wanted to let people know about a new open-source repository of analysis pipelines called [WARP][1] (for WDL Analysis Research Pipelines). It's maintained by the team at the Broad Institute that develops and optimizes data processing and analysis workflows for the Broad's production p ...
written 3 months ago by
vdauwera • 990
0
votes
1
answer
314
views
1
answers
... Hi @Irsan, I was notified of your question to the Broad’s email system. Posting the answer here so it can benefit others.
By default, Cromwell will copy the files from their storage location to the machine where execution happens. The Cromwell server just needs to be able to recognize and access t ...
written 8 months ago by
vdauwera • 990
2
votes
0
answers
409
views
0
answers
... Do you love to create content that delivers technical information in a clear and engaging way? We're looking for a scientific writer to join the Data Sciences Platform user education team at the Broad Institute, to help improve and extend the GATK docs, educational materials and related resources.
...
written 17 months ago by
vdauwera • 990
1
vote
7
answers
6.4k
views
7
answers
... That all makes sense to me. Right, the cost optimizations we use include preemptible instances, which make a huge difference. There are definitely some caveats around using those.
We have a version of the pipeline that's actually down to ~$3 and is faster, in part due to a new GATK4-native implemen ...
written 19 months ago by
vdauwera • 990
0
votes
2
answers
4.7k
views
2
answers
... Update to my answer: we now provide fully configured pipelines in a cloud platform called Terra that we built on top of Google cloud. Terra is freely accessible, with compute & storage billed directly by Google. You get a $300 google credit when you sign up for Terra so you can get a lot of work ...
written 19 months ago by
vdauwera • 990
1
vote
7
answers
6.4k
views
7
answers
... Speaking on behalf of the GATK team, we're now making all of our pipelines available on Google cloud through a platform developed at Broad called Terra. Terra is freely accessible, with compute & storage billed directly by Google. The pipelines are fully set up in workspaces that include test da ...
written 19 months ago by
vdauwera • 990
2
votes
7
answers
6.4k
views
7
answers
... 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 ...
2
votes
1
answer
542
views
1
answers
... 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 2.1 years ago by
vdauwera • 990
Latest awards to vdauwera
Scholar
23 days ago,
created an answer that has been accepted.
For A: GATK Workflow for GATK in Cancer Samples
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Scientific Technical Writer -- Help us write papers about GATK!
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Gatk Workshop Survey
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
For A: GATK Workflow for GATK in Cancer Samples
Appreciated
2.1 years ago,
created a post with more than 5 votes.
For A: Variant Calls: Freebayes vs GATK
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: GATK Workflow for GATK in Cancer Samples
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
For A: GATK Workflow for GATK in Cancer Samples
Appreciated
2.7 years ago,
created a post with more than 5 votes.
For A: Variant Calls: Freebayes vs GATK
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Gatk Workshop Survey
Teacher
2.7 years ago,
created an answer with at least 3 up-votes.
For A: GATK Workflow for GATK in Cancer Samples
Teacher
2.8 years ago,
created an answer with at least 3 up-votes.
For A: GATK Workflow for GATK in Cancer Samples
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: GATK Workflow for GATK in Cancer Samples
Teacher
2.8 years 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!
Teacher
3.2 years ago,
created an answer with at least 3 up-votes.
For A: GATK Workflow for GATK in Cancer Samples
Popular Question
5.6 years ago,
created a question with more than 1,000 views.
For Scientific Technical Writer -- Help us write papers about GATK!
Popular Question
5.6 years ago,
created a question with more than 1,000 views.
For The Gatk Has A New Website And Forum!
Scholar
5.6 years ago,
created an answer that has been accepted.
For A: GATK Workflow for GATK in Cancer Samples
Teacher
5.6 years ago,
created an answer with at least 3 up-votes.
For A: GATK Workflow for GATK in Cancer Samples
Appreciated
6.1 years ago,
created a post with more than 5 votes.
For Scientific Technical Writer -- Help us write papers about GATK!
Popular Question
6.8 years ago,
created a question with more than 1,000 views.
For Scientific Technical Writer -- Help us write papers about GATK!
Appreciated
6.8 years ago,
created a post with more than 5 votes.
For The Gatk Has A New Website And Forum!
Appreciated
7.1 years ago,
created a post with more than 5 votes.
For The Gatk Has A New Website And Forum!
Autobiographer
7.1 years ago,
has more than 80 characters in the information field of the user's profile.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1995 users visited in the last hour