Monkeypox: Divergence units in number of mutations

Hi Everyone,

Follow-up on a question posed here by @mdperry.

User was asking about how to recalibrate their SC2 tree “x-axis” to reflect divergence in “number of mutations”. There might be a few good reasons to do this for SC2.

Can this be similarly done with monkeypox using the nextstrain/monkeypox workflow?

The current workflow defaults to mutations per site as a proportion of the entire genome. Looks like there might be many good reasons for this, how should a user change this parameter to reflect the number of mutations instead?

In testing this out with monkeypox, I added the option : divergence_units = "mutations" in rule refine params and adjusted the augur refine parameters to reflect the change in units with --divergence-units mutations but it gave me an error attributed to rule definition which I couldn’t find in the workflow.

SyntaxError in line 251 of /nextstrain/build/workflow/snakemake_rules/core.smk:
Unexpected keyword divergence_unit in rule definition (core.smk, line 251)
  File "/nextstrain/build/Snakefile", line 57, in <module>

Has anyone been able to reproduce this? Showing the number of mutations between sequenced monkeypox samples might be epidemiologically relevant in characterizing and discriminating transmission dynamics (in synergy with the epidemiological context).

Are there reasons to be cautious about reflecting divergence units in number of mutations for monkeypox? @james reflected on this for SC2 a year ago here and provided some good reasons, what do folks think about doing this for monkeypox?

Thanks, Bryan

Hi Bryan. This should work. I think your problem is a syntax error in the rule definition (missing comma, indentation, or similar). Maybe also divergence_unit != divergence_units


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