I'm really liking RTG's vcfeval command, which takes in a gold standard vcf, a query vcf and a reference and outputs true positive vcf, true negative vcf, and the same for false positive, and false negative. My question is: is there some way to easily annotate the query vcf file so that each variant is annotated as TP, TN, FP and FN?
Yes, that's easy, just use `--output-mode annotate` (also check out the other output modes in case something else is more suitable to your needs).
