Quality for Invariant Sites?

amsci8

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

Geraldine_VdAuwera

Hi Amanda, unfortunately this is currently not possible, but it is on our to-do list.

ebanks

Hi Amanda, While it's true that the older version output a value for GQ, that value is not at all accurate. The fact that it was being emitted at all was a bug (which is why we stopped outputting it in subsequent versions). Please advise your colleagues not to use that value for their analyses!

amsci8

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

amsci8

Thanks, Eric! Good to know!