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Kevin Blighe
RTG vcfeval: 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?
1 answer
By default, vcfeval excludes variants that are not PASS or . in the VCF FILTER column (you can use --all-records if you want to include these).
There are other variant classes that are out-of-scope for the matching process, such as SVs, very long indels, non-variant records (i.e. GT is 0/0), etc.
If you run vcfeval in annotation mode (--output-mode annotate), the output VCFs will contain every record present on the input, with additional annotation fields indicating status, so you could see specifically which variants are being ignored.
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I would contact Len Trigg and RTG directly. He is a user on Biostars but does not appear that often. https://www.realtimegenomics.com/company/len-trigg
Kevin