If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

StrandOddsRatio computation

Hi there,
I have been struggling with the interpretation of the SOR annotation. I do get that a higher value is the sign of a strand bias and that this value is never negative.

I did read the SOR annotation documention but still cannot figure out how you calculate the SOR.

Here is one of my example where a SB is present for sure
REF + strand = 2185 reads
REF - strand = 5 reads
ALT + strand = 7 reads
ALT - strand = 2370 reads.

When I calculate "R" as indicated in the documentation, I obtain a very high value of 147 955.
But for this variant in the VCF file, SOR = 11.382

How is the 11.382 obtained ? Could you please help me in understanding the computation ?


Issue · Github
by Geraldine_VdAuwera

Issue Number
Last Updated
Closed By

Best Answer


Sign In or Register to comment.