No false positives in VQSR tranche plot
I'm doing a large variant calling project on a cohort of ~10,000 exomes. I've run into an issue with VQSR. Everything appears to be working normally except for my output tranche plot (attached), where I'm seeing no false positives. I know this is too good to be true.
From reading other posts on here, I used dbsnp_138.b37.excluding_sites_after_129.vcf , but this didn't change my plots. Some other details : my exomes were generated with different kits. While running VQSR I have tried using -L with the superset of all capture regions ( probably not the best idea) and the intersection of all capture regions (what I intend to use), but the tranche plots look the same regardless.
Using GATK v3.5. Any suggestions would be greatly appreciated.