We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Testdrive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a userfriendly interface!) without having to install anything.
Interpreting ExcessHet INFO field
Hi team,
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 pvalue?
Did I misinterpret something there?
As a result I am not so sure how to apply the filter...
Thank you
Joane
Best Answer

mshand ✭✭✭
Hi Joane,
ExcessHet is actually a phredscaled Pvalue. So when you see a value of 0, that's actually a phredscaled value. That means 10^0 = 1, this site actually has a pvalue of 1, which is exactly as you expected: a high pvalue. In order to filter things with low pvalues you'd want to choose a phredscaled value that was quite high.
Hope that helps,
Megan
Answers
Hi Joane,
ExcessHet is actually a phredscaled Pvalue. So when you see a value of 0, that's actually a phredscaled value. That means 10^0 = 1, this site actually has a pvalue of 1, which is exactly as you expected: a high pvalue. In order to filter things with low pvalues you'd want to choose a phredscaled value that was quite high.
Hope that helps,
Megan
Hi @mshand , I also trying to filter on ExcessHet. I've got the typical nagging question: how much is "quite high"? My values range from 0 to 174.
Is there a easy way to convert phredscaled to normal pvalues? (not sure I understand your 10^0 explanation from before)
Thanks,
Ana
Hi @anapaulamachado, To convert the pvalue back from phredscale you'd use this formula:
P=10^(Q/10)
So your value of 0 plugged into that formula is:
P = 10^(0/10) = 10^0 = 1
The value of 174 is:
P = 10^(174/10) = 3.98e18
As for choosing a cutoff, in our pipeline we filter anything more extreme than a zscore of 4.5 which is a pvalue of 3.4e06, which phredscaled is 54.69. So we run VariantFiltration with the filterExpression "ExcessHet > 54.69".
The more samples you have the more power you'll have to detect these kinds of artifacts so you'll filter more sites (and likewise the fewer samples you have, the fewer sites you'll be able to filter with this annotation). So you could start with 54.69 as a potential cutoff and adjust depending on your data as needed.
@mshand thanks a lot !