GATK VariantEval no concordance between dbSNP and our data
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5 months ago

Hi,

I use VariantEval to calculate the percentage of variant present in dbSNP. So when I use VariantEval, with CompOverlap I have this result in nEvalVariants:

Novelty nEvalVariants

all 28611

known 27943

novel 668

But in my VCF sample, I have 106137 variants. So my question is: Why do I have 28611 variants in VariantEval and 106137 in my VCF file ? Normally "all" line must be correspond to the total number of variants of my vcf, right ?

Any thoughts appreciated !

Thank you!

VariantEval GATK dbSNP Percentage • 133 views
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