Hi i've got some reads with a very high quality but low depth, eg 265.15 QUAL but a depth of just 16. Should I discount these?
I assume you mean variants, not reads...
No, generally speaking you shouldn't discount variants purely on the basis of qual or depth.
You may find some useful guidance regarding filtering in the Best Practices documentation, especially the presentations from past workshops.
sorry yes I did mean variants.
Thankyou very much