Population diversity with intermediate frequency

snayfach / MIDAS

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

http://dx.doi.org/10.1101/gr.201863.115

GNU General Public License v3.0

124 stars 52 forks source link

Population diversity with intermediate frequency #132

Closed azk001 closed 1 year ago

azk001 commented 1 year ago

Hi,

I'm looking for within-sample polymorphism with allele frequencies between 0.2 and 0.8. However, I noticed that MIDAS has two choices for the minimum frequency: --snp_maf and --site_maf. I'm not sure which one to use and how I can set it from 0.2 to 0.8.

Thank you!

Amanpreet.

snayfach commented 1 year ago

Use --snp_maf. The site frequency flag requires the location to have coverage in a minim % of your samples.