Inconsistent ROC reporting compared to labeled VCF

[ksw9]

Hi, I have used hap.py to measure performance and get a strange result in which at the highest value of my QQ field (QUAL = 228), a very low recall of 0.018067 is reported. This is incorrect when I examine the labeled VCF with TP and FPs, where true recall should be 0.9430894 (1044/1107).

I run hap.py with the following command: hap.py -r ${ref} $truth $query -o ${output} --set-gt hom --roc QUAL

Any suggestions would be wonderful. Thank you!

# ROC for highest QUAL value
SNP,*,*,ALL,*,QUAL,228.000000,0.018067,0.384615,0.0,0.034513,0,0,4411532,,0.000000,1107,651.000000,456.000000,.,.,1.4276315789473684,,20,10.000000,10.000000,.,.,1.0,,1087,641.000000,446.000000,.,.,1.437219730941704,,52,23.000000,28.000000,.,.,0.8214285714285714,,20,10.000000,10.000000,.,.,1.0,,32,13.000000,18.000000,.,.,0.7222222222222222,,0,0.000000,0.000000,.,.,,