Sensitivity of variant calling

Question

[anon]

Hi All,

can someone recommend for me a tool besides GATK - GenotypeConcordance module, which can calculate the variant calling sensitivity from the comparison of two .vcf files?

Many thanks!

Answer 1

[Len Trigg]

Use the vcfeval command from RTG Tools or RTG Core. It is very sophisticated in that it deals with the fact that there can be alternative ways of specifying equivalent calls (particularly when indels are involved) by performing comparison at the haplotype level. Since you are talking about sensitivity, it sounds like one of your VCFs is a "baseline" with which you want to compare the other. The output of vcfeval includes separate VCFs containing variants that are considered true positives, false positives, false negatives, as well as a data file that can be used with rtg rocplot to view an ROC curve to better help you choose filtering criteria to let you adjust your sensitivity/recall trade-off to your needs.