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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.
