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Interpreting ExcessHet INFO field
First thanks for the wonderful help and clarity of explanations on this website.
I am considering applying a filter on ExcessHet on my vcf files to have only markers that follow HWE. I understood that the ExcessHet value was the probability of getting the same or more heterozygotes as was observed unde HW conditions. But looking at my data, I get sites like this:
Scaffold_100 316384 . A C 1085470 PASS AC=55;AF=0.724;AN=76;BaseQRankSum=0.764;ClippingRankSum=0.00;DP=36981;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.9342;MLEAC=55;MLEAF=0.724;MQ=57.15;MQRankSum=0.771;QD=29.50;ReadPosRankSum=0.118;SOR=1.517 GT:AD:DP:GQ:PL 1/1:1,120:121:99:4815,322,0 1/1:1,594:595:99:24888,1748,0 1/1:0,789:789:99:33158,2371,0 1/1:4,461:465:99:19229,1157,0 1/1:2,106:108:99:4322,245,0 1/1:9,279:288:99:11278,484,0 1/1:1,265:266:99:10808,754,0 1/1:8,246:254:99:10149,462,0 1/1:5,293:298:99:12072,726,0 1/1:1,734:735:99:30363,2167,0 1/1:9,302:311:99:12455,568,0
Where ExcessHet is 0 but the site is monomorphic for the alternate allele, so following the null hypothesis of HWE there should be no heterozygote, as observed, and I should get a high p-value?
Did I misinterpret something there?
As a result I am not so sure how to apply the filter...