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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 ?

Thanks
Manon

Issue · Github
by Geraldine_VdAuwera

Issue Number
39
State
closed
Last Updated
Assignee
Array
Closed By
vdauwera

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