Add mutation context to Augur_PHB for Mpox

[emily-smith1]

:cool:

:pushpin: Explain the Request

Add mutation context to the Mpox track of the Augur_PHB workflow.

:books: Context

In Nextstrain, users have the option to annotate the Mpox tree with the G->A or C->T fraction. Previous studies have determined that these mutations may be indicative of APOBEC3 editing, which has played a role in sustained human-to-human transmission of Mpox clade IIb. A public health laboratory has requested that we add this feature to better monitor these changes.

:chart_with_upwards_trend: Desired Behavior

These data are added to the auspice_input_json file that is output from the Augur_PHB workflow, so users can annotate by this field when viewing the phylogeny in Auspice.

:information_source: Additional Information

Helpful info from the Nextstrain team:

From our monkeypox workflow, the script takes a newick tree and an "nt_muts.json" file (view code).

The nt_muts.json file is generated by an “augur ancestral” command (view).

After which, you'll need to pull out the GA_CT_fraction for each node, either by modifying the script or writing a new script (attached):

json_tsv.py.txt

[kapsakcj]

script here: https://github.com/nextstrain/mpox/blob/master/nextclade/scripts/mutation_context.py

• testing manually (not in the context of a WDL workflow) to see if this is feasible in the first place & create an auspice_input_json file with the 2 new desired options (view in auspice to confirm)
• Find a suitable docker image or create a new docker image to run the mutation_context.py script
• create WDL task for running script; test
• add this task to the augur workflow; test
• add output of this new task, which should be a mutation_context.json file to be passed into augur export command which produces the final auspice_input_json file

[kapsakcj]

to test locally:

• inputs required:
  • augur_refine.refined_tree from augur refine
  • augur_ancestral.ancestral_nt_muts_json from augur ancestral
• mutation_context.py from here: https://github.com/nextstrain/mpox/blob/master/nextclade/scripts/mutation_context.py

test with this command:

python3 scripts/mutation_context.py \
  --tree results/hmpxv1/tree.nwk \
  --mutations results/hmpxv1/nt_muts.json \
  --output mutation_context.json

This should output a mutation_context.json file

Can skip augur_translate step

Then test with augur export with the mutation_context.json added as an input for node_jsons

[emily-smith1]

This has been tested successfully by a public health partner, who suggested we include detailed documentation on what the numbers in the legend represent and an example use case.