Automatic clone_threshold is 'NA'. Consider setting --clonal_threshold manually. about airrflow HOT 2 OPEN

Hi @petemeng ,
yes this is a desired behaviour of airrflow, that it will notify the user if the clonal threshold could not be set automatically.
You can find a report under results/clonal_analysis/find_threshold/index.html that shows a plot of the hamming distance distribution that can be used to find the appropriate threshold manually according to your dataset.

For example, for this analysis:

A threshold at around 0.11 seems to be able to separate sequences forming clones from singletons.
A more detailed explanation on how this method works, can be found on the Immcantation Shazam vignette: https://shazam.readthedocs.io/en/stable/vignettes/DistToNearest-Vignette/

from airrflow.

Thank you for your answer.

from airrflow.