/home/Softs/gatk-126.96.36.199/gatk VariantAnnotator -R "/MyData/Resources/human_g1k_v37.fasta" -V fam.vcf -A PossibleDeNovo -O fam.denovo.vcf -ped fam.ped
I have VCF with trios/quads and I want to detect denovo variants so I used VariantAnnotator w/ the above command and had a question. After running it, the header specify how the calls were made :
##INFO=<ID=hiConfDeNovo,Number=1,Type=String,Description="High confidence possible de novo mutation (GQ >= 20 for all trio members)=[comma-delimited list of child samples]">
##INFO=<ID=loConfDeNovo,Number=1,Type=String,Description="Low confidence possible de novo mutation (GQ >= 10 for child, GQ > 0 for parents)=[comma-delimited list of child samples]">
(Btw, this information is not present here https://gatk.broadinstitute.org/hc/en-us/articles/360036889772-PossibleDeNovo maybe it should?)
So I ran it on my files and looked at my variants. And I found one which wasn't called as denovo, but, to my understanding, it should.
12 2721137 . C T 41828.10 GT:AO:DP:GQ:QA:QR:RO 0/0:0:13:59:0:456:13 0/0:1:3:1:33:81:2 0/1:3:10:54:94:210:7 0/0:0:91:99:0:2777:91
First sample is the father, the second is the mother, third is the proband and fourth is an unaffected sibling.
Why wasn't this variant called as LoConfDeNovo? Parent's GQ are 59 and 1 (>0) and proband is 54 (>=10).
What am I missing?
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