Forum thread to discuss GATK Germline tools
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GATK Team Out of Office
The GATK Team is out of office November 26-29 and will not be able to respond to questions. Feel free to continue to interact with other users and help each other resolve questions. If your questions are not answered, then re-post them starting November 30 with [Repost] in the title and we will get to them once we return.
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Got a problem?
- Search using the search box at the top of the page, e.g. using the error message.
- Try the latest version of tools.
- When reporting a problem, include tool and Java versions.
- Tell us whether you are following GATK Best Practices.
- 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.
- For tool errors, include the error stacktrace as well as the exact command.
- For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
- For weird results, include an illustrative example, e.g. attach IGV screenshots.
Did we ask for a bug report?
Then follow these instructions.
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