The current GATK version is 3.7-0
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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.

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Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

About "Ask the team"

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
edited January 2013 in Ask the GATK team
This is the place to post any questions, problems or bug reports for the GATK development team to look at.

We try to respond within a reasonably short amount of time, but keep in mind that we are not support agents -- we are programmers and scientists, with code to write and data to analyze. In the same spirit, because our resources are limited and our time precious, we ask that you please consult all available sources of information in the GATK Guide and previous posts in this forum before posting your question here, and above all, refrain from posting problems that are clearly identified as USER ERRORS in the GATK's output. Thank you!

We also welcome discussions and responses from everyone in the user community. If you know something, say something!
Post edited by Geraldine_VdAuwera on

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    edited November 2012

    Please note that this post is intended to explain what this section of the forum is about, not for asking actual questions about the software. If you have a question that you would like to address to the GATK development team, please use the big "Ask a Question" button at the top left of this page to create a new post.

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