Can a command in RTG (or elsewhere) annotate the TP/TN/FP/FN's produced from RTG's vcfeval?

Question

[Tails]

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?

[Kevin Blighe]

Tagging the man himself, Len Trigg

Answer 1

[Len Trigg]

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).

[Kevin Blighe]

Thanks Len