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☞ Got a problem?
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
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