I compared HaplotypeCaller and UnifiedGenotype of the latest version of GATK (2.7-4) on the same NA12878 trio. It seems HC missed some true variants (specifically, 7 out of the 49 experimentally validated de novo SNVs are missed). I guess this might be partly due to HCMappingQualityFilter, because the log says ~9% of the total reads have been filtered by this filter, and it looks there is not such a filter in UnifiedGenotyper. I wonder is there a safe way to relax HCMappingQualityFilter (default 20) to achieve a better sensitivity for HC?
Thanks in advance!
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