HW3: what is considered rare?

[dfhannum]

This isn't a code based question. In the homework it states:

Extract the AF_EXAC data to determine the rarity of the variant If the disease is rare: return an a list of associated diseases If the disease is not rare: return an empty list

I am unsure of what cutoff to use for a rare variant. People in my lab said they were thinking around 1%, or using a minor allele cutoff depending on the size of the dataset. For this we would use frequencies since that is what we get from AF_EXAC. Maybe I missed this somewhere in the notes, but I couldn't find a cutoff to use for this.

[CooperStansbury]

The Notebook is slightly less informative than the Canvas assignment. From the Canvas assignment:

_If the variant is rare (value for the AFEXAC key < 0.0001)

[dfhannum]

THANKS!!