pv4 values interpretation
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Entering edit mode
6.3 years ago
cmatho ▴ 30

Hello I am having some trouble interpreting the pv4 values I get in my .vcf files I know that pv4 field shows:

PV4: P-values for 1) strand bias (exact test); 2) baseQ bias (t-test); 3) mapQ bias (t); 4) tail distance bias (t)

But I am not sure what this means, here I have one example

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT
chr2           47416318 .G  A   225.009 .            DP=1264;VDB=0;SGB=-0.693147;RPB=0.192165;MQB=1;MQSB=1;BQB=0.414088;MQ0F=0;AF1=0.5;AC1=1;DP4=385,218,411,199;MQ=60;FQ=225.007;PV4=0.204527,1,1,1    GT:PL   0/1:255,0,255


In this case if my strand bias is 0,2 this means this is the probability that I have strand bias? Or p value meaning that p values over 0.05 mean they are not different???

From the Dp4 values I can see that the forward strand is more read for the reference and the altered base too, this would mean I have strand bias??

About the other parameters baseQbias, mapQbias and tail distance bias I have no idea!! Can someone please advice on the meaning of this parameters and the expected values to trust a call?

pv4 vcf strand bias baseQbias SNP • 2.0k views
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Entering edit mode
20 months ago

Hi, I am not sure if you had figured out this but I am looking to understand PV4 and VCF file specs document does not really explain this field much, unfortunately! Let me know if anyone has an answer. TIA