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

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?

sequence genome
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updated by Len Trigg Len Trigg • written by Tails Tails

1 answer

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).

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written by Len Trigg Len Trigg

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