This is a kind of follow-up inspired by the very good question/answers I read in "How to calculate sensitivity/selectivity of an algorithm that returns locations of possible matches?"
My goal is to evaluate the Sensitivity/Specificity of an indel detection method.
I have a "gold standard" VCF file (ref.vcf) that states where are exactly the insertions and deletions in my genome. And of course, my indel detection method produces its own VCF file (let's call it test.vcf).
To calculate the True Positives, I detect the intersection of test.vcf and ref.vcf (I use exact intersection for the sake of simplicity for now). The False Positives, are the features in test.vcf that are not in ref.vcf. And False Negatives are the features in ref.vcf that are not in test.vcf.
But how would you calculate the True Negatives? I just can't use the number of positions left (too big number!).