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How to evaluate a call set when no true snp set is available?
I would like to know how to evaluate a call set when no true snp set is available. Are there recommendations? Certain values one can look at? VariantEval seems to focus on comparing with a reference of known variants. But maybe there are at least a couple of basic values that one can evaluate?
Also, is there a ballpark percentage of SNPs that is usually filtered by the hard filtering recommendations? I am aware that you cannot give me a precise number here but I would like to know if I should expect 10-30 % to get kicked out or more like 60-80 % to get kicked out.
Thanks so much!!