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Forum: Bioinformatics 10-23-2020, 12:07 PM
Replies: 0
Views: 615
Posted By vdauwera
Lightbulb New repo sharing Broad production workflows for data processing & analysis

(cross-posting from Biostars)

Hi all, I just wanted to let people know about a new open-source repository of analysis pipelines called WARP (https://github.com/broadinstitute/warp) (for WDL...
Forum: Bioinformatics 01-04-2016, 01:34 PM
Replies: 2
Views: 4,669
Posted By vdauwera
This is addressed in the GATK documentation: ...

This is addressed in the GATK documentation:

https://www.broadinstitute.org/gatk/guide/article?id=59

Feel free to ask any other GATK-related questions in the GATK forum; we're there to help.
Forum: Bioinformatics 12-10-2014, 01:16 PM
Replies: 0
Views: 1,140
Posted By vdauwera
Question Which GATK tools should we not remove in future versions?

As posted here: https://www.broadinstitute.org/gatk/blog?id=4923

We are going to remove a number of tools from future versions of GATK. We would like to hear from you if you use any of the tools...
Forum: Bioinformatics 05-05-2014, 03:24 PM
Replies: 14
Views: 4,614
Posted By vdauwera
That's completely fine actually, the...

That's completely fine actually, the BP_RESOLUTION gvcfs are also a valid input for the joint genotyping step. I'll update the documentation to be more accurate and inclusive. Feel free to post any...
Forum: Bioinformatics 05-04-2014, 09:27 AM
Replies: 14
Views: 4,614
Posted By vdauwera
Sure, if you want a call for every single...

Sure, if you want a call for every single position (instead of averaged blocks, which are used to compress the information in order to minimize file size) you just change -ERC GVCF to -ERC...
Forum: Bioinformatics 05-02-2014, 10:26 AM
Replies: 14
Views: 4,614
Posted By vdauwera
Oh, if you have multiple samples, you can just...

Oh, if you have multiple samples, you can just call each in turn using the GVCF mode, then you do the joint genotyping to get a single multi-sample VCF with the results.

If your problem is that...
Forum: Bioinformatics 05-02-2014, 07:12 AM
Replies: 14
Views: 4,614
Posted By vdauwera
Hi Muriel, What you want is to run the...

Hi Muriel,

What you want is to run the GATK's HaplotypeCaller in GVCF mode, with the arguments --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 added to your...
Forum: Academic/Non-Profit Jobs 04-16-2014, 02:15 PM
Replies: 0
Views: 1,558
Posted By vdauwera
Scientific Technical Writer at the Broad Institute - Help us write papers about GATK!

We have a problem: we have a truckload of material sitting around waiting to be published, but no time to actually write the papers. So we're looking for someone who will help us convert this...
Forum: Bioinformatics 01-23-2014, 10:01 AM
Replies: 1
Views: 1,505
Posted By vdauwera
There are two ways to deal with this. One is to...

There are two ways to deal with this. One is to use the EMIT_ALL_SITES option of UnifiedGenotyper and enable calculation of reference PLs. The other, which is better, is to call variants with...
Forum: Bioinformatics 11-25-2013, 03:25 PM
Replies: 2
Views: 7,000
Posted By vdauwera
Hi there, These tools have evolved slightly...

Hi there,

These tools have evolved slightly over the past few months, so make sure to read the latest documentation here: http://www.broadinstitute.org/gatk/guide/best-practices

Also, look at...
Forum: Bioinformatics 11-19-2013, 08:16 AM
Replies: 2
Views: 4,442
Posted By vdauwera
Exclamation Hi there, If you consider the...

Hi there,

If you consider the HaplotypeCaller output to be your final file, you're not really following Best Practices... As indicated in the GATK documentation, the output of HaplotypeCaller is a...
Forum: Bioinformatics 11-18-2013, 08:58 AM
Replies: 6
Views: 2,279
Posted By vdauwera
Ah, you've caught me in between two updates of...

Ah, you've caught me in between two updates of the website -- that page is no longer available, but I haven't put up its replacement yet. My bad. In the meantime I recommend using...
Forum: Bioinformatics 10-18-2013, 01:02 PM
Replies: 6
Views: 2,279
Posted By vdauwera
Well, we certainly wouldn't want that! Glad...

Well, we certainly wouldn't want that!

Glad you found what you needed :)

(sorry if I robbed you of a great excuse to tell your PI you couldn't find any answers and couldn't get whatever they...
Forum: Bioinformatics 10-18-2013, 12:29 PM
Replies: 6
Views: 2,279
Posted By vdauwera
LOL ok then. If you need to access specific...

LOL ok then. If you need to access specific articles, they are still accessible via the forum (although the layout is a little screwy because the css is not loading).

For argument lists, you can...
Forum: Bioinformatics 09-20-2013, 06:46 AM
Replies: 4
Views: 4,036
Posted By vdauwera
See the GATK Best Practices (newly redesigned for...

See the GATK Best Practices (newly redesigned for clarity) here:

http://www.broadinstitute.org/gatk/guide/best-practices
Forum: Bioinformatics 09-10-2013, 10:30 AM
Replies: 1
Views: 2,121
Posted By vdauwera
Answered on the GATK forum here: ...

Answered on the GATK forum here:

http://gatkforums.broadinstitute.org/discussion/comment/8863/#Comment_8863
Forum: Events / Conferences 08-28-2013, 08:52 AM
Replies: 0
Views: 1,718
Posted By vdauwera
Exclamation GATK workshop Oct 21-22 to coincide with ASHG conference

Hi all,

The next GATK workshop will take place at the Broad in Cambridge, MA, on October 21-22 (2013), just before the start of ASHG Boston.

If you're going to be in town for ASHG, be sure to...
Forum: Bioinformatics 08-21-2013, 07:32 AM
Replies: 10
Views: 4,622
Posted By vdauwera
You'll need to add the platform information to...

You'll need to add the platform information to your read groups. You can use Picard tools' AddOrReplaceReadGroups (http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadGroups) to...
Forum: Bioinformatics 04-30-2013, 07:03 PM
Replies: 6
Views: 1,217
Posted By vdauwera
The GATK tool you're thinking of is probably...

The GATK tool you're thinking of is probably FastaAlternateReferenceMaker: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_fasta_FastaAlternateReferenceMaker.html
Forum: Bioinformatics 04-29-2013, 07:56 PM
Replies: 6
Views: 1,217
Posted By vdauwera
Hi there, can you clarify what you mean by...

Hi there, can you clarify what you mean by "convert this into actual new genes"? Are you trying to get the separate haplotype sequences for your sample output as sequence files, perhaps?
Forum: Illumina/Solexa 04-17-2013, 06:40 PM
Replies: 58
Views: 42,389
Posted By vdauwera
Lightbulb FYI the GATK callers now include a fractional...

FYI the GATK callers now include a fractional downsampler specifically designed to compensate for contamination (regardless of origin, which can be lab prep, machine etc). It is activated by default...
Forum: Bioinformatics 04-09-2013, 05:55 PM
Replies: 3
Views: 1,624
Posted By vdauwera
Lightbulb The syntax looks weird because that is a very old...

The syntax looks weird because that is a very old version, and the syntax has changed since. I strongly recommend you upgrade to a more recent version, Opulcy. The old version is buggy and slow; the...
Forum: Bioinformatics 03-19-2013, 09:39 AM
Replies: 1
Views: 1,300
Posted By vdauwera
Lightbulb You should look up the meaning of these arguments...

You should look up the meaning of these arguments in the technical documentation for GATK. For example, you can find the description of -dcov here:...
Forum: Bioinformatics 03-18-2013, 06:36 AM
Replies: 1
Views: 2,627
Posted By vdauwera
Lightbulb It depends a lot on how you're running it (e.g....

It depends a lot on how you're running it (e.g. whole genome or exome targets only?) and what kind of machine you're running on (e.g. personal computer or server?).

For more details and advice on...
Forum: Bioinformatics 03-08-2013, 09:13 AM
Replies: 10
Views: 2,390
Posted By vdauwera
HaplotypeCaller cannot handle pooled samples yet,...

HaplotypeCaller cannot handle pooled samples yet, so for now you should use UnifiedGenotyper.
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