It looks like you're new here. If you want to get involved, click one of these buttons!
I have a set of 48 exomes which were analysed according to the best practices (using GATK-2.2-3 and HaplotypeCaller). According to the VQRS I have this first level of "uncertainty":
##FILTER=<ID=VQSRTrancheBOTH90.00to99.00,Description="Truth sensitivity tranche level for BOTH model at VQS Lod: -1.3455 <= x < 2.62">
that sets filter=PASS for variants with VQSLOD >= 2.62.
I also have an external validation of some SNPs, 3 out of 20 have a VQSLOD lower than 2.62 (1.24, .1.37 and 1.69). Now the question: should I trust the validation and set the filter to, say, VQSLOD >= 1.2 or keep the GATK filter? What is your experience about this?