search

omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
96 stars 22 forks source link

Custom Annotations, common and lowfreq #99

Closed gbloeb closed 2 years ago

gbloeb commented 2 years ago

Is there a reason you made separate annotations for functional annotations with common and low frequency variants? Do you recommend doing this for other functional annotations? What MAF cutoff did you use? I scoured the paper and did not see the explanation--sorry if I'm missing it!

gbloeb commented 2 years ago

I should have read Gazal et al. Nature Genetics 2018 before asking...seems like MAF 5% is the cutoff and that other than coding variants, probably doesn't matter very much.