number of variants reported by vcfeval is not equal to actual number of variants.

Hello community,

I am running the rtg-tool vcfeval as follow:

rtg vcfeval  
--baseline baseSnps.vcf.gz 
--calls calledSnps.vcf.gz 
--output rtg-results 
--template ref.sdf 
--sample "Macrogen-48-0511,48-0511" 
--output-mode "split"

The ref.sdf is generated from GRCh37.
Both VCF files were based on this build.

I noticed however, that the number of variants reported by this tool is a lot less that the actual number of variants found in both vcf files.

baseSnps.vcf.gz contains 378285 variants
calledSnps.vcf.gz contains 1125224 variants

However, looking at the summary:

Threshold  True-pos-baseline  True-pos-call  False-pos  False-neg  Precision  Sensitivity  F-measure
----------------------------------------------------------------------------------------------------
     None            3508339        3509333     525719      52825     0.8697       0.9852     0.9238

TPbase + FN = 3508339 + 52825 = 3561164
TPcall + FP = 3509333 + 525719 = 4035052

Is there something, I'm missing?