Question: Fisher strand (FS) 0?
gravatar for joshua.motelow
3 days ago by
joshua.motelow0 wrote:


Can you help me understand why the following variant has a fisher stand (FS) phred-scaled P value of 0?

11      65107949        .       G       A       48.06   PASS    AC=1;AF=0.500;AN=2;DP=73;FS=0.000;MQ=245.31;MQRankSum=7.260;QD=0.66;ReadPosRankSum=4.771;SOR=0.633;FractionInformativeReads=1.000;R2_5P_bias=-4.567 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB        0/1:42,31:0.425:73:25,19:17,12:47:83,0,50:4.806e+01,8.983e-05,5.300e+01:0.00,34.77,37.77:25,17,18,13:24,18,14,17

I know FS isn't calculated when, for example, there are no forward (or reverse) strands. Are there other situations when it's not calculated?

Please let me know if there's any additional information that would be helpful

Thanks very much

fisher strand gatk fs • 67 views
ADD COMMENTlink modified 2 days ago by finswimmer13k • written 3 days ago by joshua.motelow0

What tool generated this data? Including the command line can be helpful too.

From what I can interpret of the data you posted originally, it looks like quite a normal HET, with basically balanced reads. What did you expect of the FS field?

ADD REPLYlink written 3 days ago by karl.stamm3.6k

This one seems to say that high FS indicates strand bias, and possibly false positives from low coverage regions. Makes sense that a position with "25,19:17,12" has really 0 apparent strand bias.

ADD REPLYlink written 3 days ago by karl.stamm3.6k

While it seems fairly balanced, I'm surprised that it is 0.000 (a p-value of 1). A p-value of 0.999 would still generate a phred scaled p value of 0.004.

ADD REPLYlink modified 3 days ago • written 3 days ago by joshua.motelow0

p-values are not effect sizes. Anything p>0.2 is equivalent to saying 'no evidence' you shouldn't judge the difference between a p=0.5 and a p=0.9 to mean anything at all. They tend to get conflated with strength of association, because in introductory statistics they may appear to be correlated, but in complicated situations like sequencing quality especially, 'all other things equal' does not hold. So I wouldn't be surprised if the GATK folks just have the system fail to FS=0 because calculating the p=0.999 is a waste of time.

ADD REPLYlink written 3 days ago by karl.stamm3.6k
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