Extract diversity data

Hello, I would like to have the diversity data of my analysis in excel, but within the files in the results folder I do not see any file with this information.
Is there any way to get this data?


Hi David, can you explain what exactly you mean by diversity data? Do you mean the data as presented in the entropy panel when viewing an auspice.json like this?

What workflow do you run? Your own augur pipeline or do you just view a build using auspice?

yes, I would like to have that data to obtain an average and obtain the places with the highest entropy, since doing this only with the view is tedious.

I use normal workflow.

Open your auspice.json file in auspice.us, press the d key and select Genetic diversity data.

Then you get your diversity data in TSV format.

I hope that helps!

Unfortunately, I think it’s just what one sees at the moment, so if you want all 4 combinations of {AA,NT}x{entropy,events} it takes 4 downloads.