No FP or TP calls about truvari HOT 2 CLOSED

From the information provided my only assumption is that 06_sv/CD_3032_Cache.hg19.sv.vcf.gz is empty. The line 9655 chunks of 20041 variants Counter({'__filtered': 10400, 'base': 9641}) says that there are 20041 variants analyzed and the line Zipped 20041 variants Counter({'base': 20041}) says that all the variants are in the baseline vcf. If there were comparison variants, the lines would say something like Counter({'comp': 12345....

Have you checked the comparison vcf?

from truvari.

It's definitely not empty. I figured it out. It turns out I was using the wrong reference, that is, I was using hg19 from UCSC. I used the one from the NIST website directly and everything worked.

from truvari.