The current GATK version is 3.8-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

How does the community manage custom walkers?

I was wondering how other people package and manage any custom walkers they write? I wrote my first walker last week, and am now trying to figure out the best way to make it available to my team and keep it up to date with new versions of GATK. I do my development on a laptop and analysis on a cluster, so I have to sync the code somehow. I can think of two possibilities, it's unclear to me which is best:

Package a Monolithic jar

Pros: Makes distribution very easy, guarantees that there are never version compatibilities

Cons: Well, I haven't been able to do it yet. I can't quite figure out how to supply a package .xml file that will import my classes into GenomeAnalysisTK.jar (or Queue.jar, for that matter). Also, I think the version number will change when I customize it, and customers/collaborators may get confused about a non-standard version number (if they notice)

Create a "Custom Walker" jar

Pros: I know how to do it. It won't change the GATK version, so the log files won't look different

Cons: I'll have to remember to include my jar on the classpath (or set an environment variable, I suppose). It's possible to encounter version incompatibilities, for instance if I want to test 3.0 but use 2.8 for production

Now that I think it through, maybe the cons of the custom jar aren't as bad as I thought. Does anyone else have any experience with Custom Walker maintenance/deployment? How did you do it?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Phil,

    We have been porting GATK over to the Maven build system, which the softengs assure me will make this all much easier (starting in 3.0). We'll make sure to document the new build / distribution process. Eta next week.

  • pdexheimerpdexheimer Member, Dev

    You know, I've seen you mention that several times now, and I still spent several hours tracing and learning build.xml. Thanks, Geraldine - I'll table this for a day or so

    The larger question stands, though - does anyone feel like they're managing custom walkers well? What kind of problems/solutions have people encountered?

Sign In or Register to comment.