Hello!
I have generated qq plot for my gwas using hl.plot.qq() function but i got a plot where looks inflated despite that lambda is 0.92. Do you have any insights about what the possibilities behind this?
Does hail have a function to calculate lambda?
Hi @Ola,
You can see the implementation of our lambda method here. It’s quite simple.
Note that it uses a non-deterministic approximate method for efficiency, so if you’re observing large differences in the lambda estimate between runs, that would be a bug we would need to address. Likewise if you have evidence that the computed lambda is wrong (beyond just a small approximation error).
Otherwise, we (the Hail developers) aren’t stats experts, and can’t offer help on interpreting the lambda value. But maybe another user would be able to chime in!