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.
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 ?