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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

# Haplotype caller

Member
edited July 2012

Hi,

The version of GATK i have installed is unable to find command "HaplotypeCaller", i have the following versions of GATK installed.
version 2.0-0-gb142977 (built from git)
version 2.0-0-g4c0ffd4 (GenomeAnalysisTKLite.jar)
version 1.6-13-g91f02df

Errors out saying cannot find walker with name HaplotypeCaller.

Thanks
Uday

Post edited by Carneiro on
Tagged:

Hi Uday,

The HaplotypeCaller is available only in the full release of the GATK (starting from 2.0), whereas you only have the lite version. I've just pushed in a patch so that in the future you will get a warning stating this when trying to use full-version-only walkers from the lite build of the GATK.

• Member

Is version 2.0 released ? If not when do you think it will be released ? Also if i have a version of GATK built from git, should that be containing this walker.

Version 2.0 has been released, yes; please see the Downloads page for links to the available packages.

The public git repository contains the source corresponding to GATK Lite, which does not contain the HaplotypeCaller walker. If you want to use it, you need to download the full version, but be aware its use is limited to non-commercial purposes at this time. Please see the GATK 2.0 Announcement on this forum for details.

• Member

I am sorry but i was unable to find version 2.0 . I looked at the download page and ftp

May be i am looking in the wrong place, could you please point me in the rite direction.
Thanks

You need to look on the new website -- you should see the navigation bar at the top of this page. All downloads are clearly marked on the Downloads page.

• North CarolinaMember

Is the haplotype caller going to be added to the git repository at some point?

Hi @williamw,

The HC is available in the gatk-protected repository here: https://github.com/broadgsa/gatk-protected