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?
