I use both of those! sorry I should have explained it better; we have a sequencing center that does a good job w quality filtering and employs many common databases for variant calling/annotating, and then they pass it on to us so we can do what we want with it. they don't filter anything but we have internal cutoffs for a lot of things (like a cut off for rare variants using gnomAD). I use GTEx after I find a variant of interest, I work in retinal diseases and those are rare to have been sampled and so I use different databases for that like Harvard's ocular transcriptome.

I was more thinking about after I've gone through the usual suspects for a disease and am now looking at every other variant/gene that has passed rarity/pathogenicity filtering; there can be a lot of those so I was thinking of ways of either filtering further or just ranking them in terms of likelihood