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?