vcfeval: baseline total value changes while --all-records is used

[Alexandra Vatsiou]

Hello,

I am launching vcfeval using --all-records and while the total number of variants in the baseline is 5537943 , in the summary output from rtg-tools I get only 5410837 (TP+FN) and I also noticed that this value might change based on the called vcf. 

Is this because some variants are excluded due to missing GQ values? 

Here is an example of the command I use:

rtg vcfeval -c called.vcf.gz -b /baseline.vcf.gz --no-gzip --decompose -t REF -o output --sample sample1,sample2 --all-records

Thanks,

Alexandra

[Len Trigg]

Hi Alexandra,

Lack of GQ values should not be a problem. --all-records will include variants marked as failing filters, but there may still be other reasons why variants are not included in matching - usually for reasons such as the variant being too long, the GT having unexpected ploidy or using an invalid allele. Another possibility is that occasionally local regions with a very high number of variants may be too complex to evaluate, causing those regions to be skipped. Both of these types of events should be listed in the vcfeval log file.

Cheers,

Len.

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