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:
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 !