Clarification of the output (fp.vcf) and the FP field in the summary.txt about truvari HOT 2 CLOSED

Your expectations are correct. The VCFs should have as many entries as the counts in the summary.txt. For example, in our testing infrastructure, we see:

$ head summary.txt
{
    "TP-base": 7,
    "TP-call": 8,
    "FP": 9,
    "FN": 4,
    "precision": 0.47058823529411764,
    "recall": 0.6363636363636364,
    "f1": 0.5410628019323671,
    "base cnt": 11,
    "call cnt": 17,
$ grep -vc "#" *.vcf
fn.vcf:4
fp.vcf:9
tp-base.vcf:7
tp-call.vcf:8

If those two commands (head/grep) aren't matching up, I expect there's some sort of problem. Could you double check that those two commands aren't matching up and if not, provide example data so that I can recreate the problem.

from truvari.

Hi! Thanks for your quick reply. That makes sense, I just checked as you suggested using head/grep and I now can't seem to recreate the problem - so I will close the issue for now :) Many thanks for your quick help!

from truvari.