Merge pull request #66 from nextstrain/reduce-inference-in-cattle-out…

…break Reduce inference in cattle outbreak
nextstrain · Jun 27, 2024 · 5763ebb · 5763ebb
2 parents 96d4f9d + 0ad7d7a
commit 5763ebb
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/Snakefile.genome b/Snakefile.genome
@@ -248,14 +248,16 @@ rule traits:
     output:
         node_data = "results/{build_name}/genome/traits.json"
     params:
-        columns = 'division'
+        columns = 'division',
+        sampling_bias_correction = 5
     shell:
         """
         augur traits \
             --tree {input.tree} \
             --metadata {input.metadata} \
             --output {output.node_data} \
             --columns {params.columns} \
+            --sampling-bias-correction {params.sampling_bias_correction} \
             --confidence
         """
 

diff --git a/config/auspice_config_h5n1-cattle-outbreak.json b/config/auspice_config_h5n1-cattle-outbreak.json
@@ -119,7 +119,8 @@
   "display_defaults": {
     "map_triplicate": false,
     "color_by": "host",
-    "geo_resolution": "division"
+    "geo_resolution": "division",
+    "distance_measure": "div"
   },
   "filters": [
     "host",