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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.

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Then follow instructions in Article#1894.

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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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Quality for Invariant Sites?

amsci8amsci8 USAMember Posts: 14

Hello,
I have been successfully using the GATK pipeline and Unified Genotyper to call snps. However, I really need GQ scores for invariant sites as well as variant sites.

Currently at invariant sites, only GT and DP are outputted. Is it possible to also get GQ for these sites? I can't seem to find how to do this.

Thank you!
Amanda

Best Answers

Answers

  • amsci8amsci8 USAMember Posts: 14

    Thanks, Geraldine!

    Interestingly, colleagues of mine who are using an older version (before 1.6) DO get quality for invariant sites. Any thoughts there?

    Thanks!
    Amanda

  • amsci8amsci8 USAMember Posts: 14

    Thanks, Eric! Good to know!

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