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Quality for Invariant Sites?

amsci8amsci8 USAPosts: 14Member

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!

Best Answers


  • amsci8amsci8 USAPosts: 14Member

    Thanks, Geraldine!

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


  • amsci8amsci8 USAPosts: 14Member

    Thanks, Eric! Good to know!

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