Question: Can a command in RTG (or elsewhere) annotate the TP/TN/FP/FN's produced from RTG's vcfeval?
1
gravatar for Tails
11 months ago by
Tails60
New Zealand
Tails60 wrote:

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 • 295 views
ADD COMMENTlink modified 11 months ago by Len Trigg1.5k • written 11 months ago by Tails60

Tagging the man himself, Len Trigg

ADD REPLYlink written 11 months ago by Kevin Blighe69k
2
gravatar for Len Trigg
11 months ago by
Len Trigg1.5k
New Zealand
Len Trigg1.5k wrote:

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).

ADD COMMENTlink written 11 months ago by Len Trigg1.5k

Thanks Len

ADD REPLYlink written 11 months ago by Kevin Blighe69k
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