The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

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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 2.9.0 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.

Licencing questions

I have two licence questions. First of:

There are two licence notes in BaseTest.java. I'm assuming that the top one is the one that should be viewed as currently in use. Is this correct?

Secondly, under which licence are the test resources made available. Am I'm free to use and redistribute these? I'm asking since I'm in the process of refactoring my pipeline project to use GATK as a external dependency, but some of the tests I've written use the files provided with the GATK as a resource, and I'd like to keep them and distribute them with the project as I've done before in my GATK fork.

Best Answers

Answers

  • Johan_DahlbergJohan_Dahlberg Posts: 96 ✭✭✭

    Great. Thanks!

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