Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

Quality for Invariant Sites?

amsci8amsci8 Posts: 3Member

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

Sign In or Register to comment.