diff --git a/Snakefile.genome b/Snakefile.genome index a1a63e9..e285c37 100644 --- a/Snakefile.genome +++ b/Snakefile.genome @@ -248,7 +248,8 @@ rule traits: output: node_data = "results/{build_name}/genome/traits.json" params: - columns = 'division' + columns = 'division', + sampling_bias_correction = 5 shell: """ augur traits \ @@ -256,6 +257,7 @@ rule traits: --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 index 9d9b226..37f539a 100755 --- 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",