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dcittaro
Posts: 13Member ✭
Hi all, I've somewhere in this site that before VQSR the FP rate is expected to be around 10% (I guess for UnifiedGenotyper). Are there some updated statistics for VQRS? For HaplotypeCaller? For Exome/WG data? Another thing: we apply VQRS on all our analysis, we are trying to collect some validation statistics. We suspect that most of the FP have some particular "culprits" in VQRS (especially QD and MQ). Do you have some data about this? Best
d
Geraldine_VdAuwera
Posts: 2,239 admin
It depends rather a lot on your data and what you're using as validation (for true/false assessment). We are currently working on new approaches to benchmark our tools for sensitivity and specificity but results are not yet ready for prime time. We'll have some teaser plots showing the latest improvements in UG and HC in the release highlights for 2.4 (ETA a week or two). Re: culprits, you can get a lot of info from the recalibration plots. Good luck!
