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SB flag in vcf file
again, thanks a lot for the amazing workshop in Brussels!
I have a question on dealing with strand bias, regarding the SB flag in the vcf file:
The value of SB (strand bias) is calculated by Fisher exact test, using a 2X2 table that contains the reference, non-reference, fwd and reverse depths. Playing a little with the numbers given to Fisher exact test through web calculator I noticed that combinations which seem as clear strand bias receive non-significant value (e.g. 30,1,110,2 for ref-fwd, ref-reverse, non-ref-fwd, non-ref-reverse receive p-value of 0.52 or 2.84 when phred-scaled).
Such variant are therefore considered as unbiased.
The cases that are defined as bias are ones where 3 out of the 4 values are similar to each and only one is extremely different.
As far as I understand, cases as the one I mentioned should be referred as biased. Do you recommend using this strand bias value and filter variants based on it?