I have 33 samples (VCF files) resulted from HaplotypeCaller and like to evaluate them using dbSNP as a comp to get concordance_rate, sensitivity, and specificity. One way is to evaluate each sample separately. Another approach is to combine all 33 files using "CombineGVCFs" and then evaluate one VCF file. Which of these 2 methods do you think is feasible and acceptable for variant evaluation? why? Thanks
In the following article you explained about sensitivity, descripency rate and concordant rate. What about Specificity rate?
Could you please introduce an article or a reference to explain each parameters measures in the output of "VariantEval". Thanks
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