search

pblischak / HyDe

Hybridization detection using phylogenetic invariants
http://hybridization-detection.readthedocs.io
GNU General Public License v3.0
41 stars 15 forks source link

Input need to filter minor allele frequence SNP? #18

Open sandyplus opened 3 years ago

sandyplus commented 3 years ago

Dear @pblischak ,

Is it necessary to filter SNPs with minor allele frequency (MAF) < 0.05? I want to make input from VCF. I wonder whether the MAF SNP will bias the results of HyDe or not?

Best regards, Sandy

pblischak commented 3 years ago

Hi Sandy,

For the tests that I've done I've never done any filtering based on minor allele frequencies. I think it's possible that it would affect the results -- you would probably just lose a little bit of power. I'd actually be curious to know if you find a difference when you run HyDe with or without an MAF filter.

I realize that's not super helpful but please let me know if you have any other questions -- thanks!