Merge pull request #110 from nextstrain/james/cattle-outbreak-clock-f…

…ilter Cattle outbreak clock filter
nextstrain · Dec 10, 2024 · 0780396 · 0780396
2 parents ec2b17d + 871a0de
commit 0780396
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Showing 3 changed files with 8 additions and 1 deletion.
diff --git a/Snakefile b/Snakefile
@@ -203,7 +203,9 @@ def refine_clock_rates(w):
     return f"--clock-rate {info[w.segment][0]} --clock-std-dev {info[w.segment][1]}"
 
 def refine_clock_filter(w):
-    filter = get_config('refine', 'clock_filter_iqd', w)
+    filter = get_config('refine', 'genome_clock_filter_iqd', w) \
+        if w.segment=='genome' \
+        else get_config('refine', 'clock_filter_iqd', w)
     return f"--clock-filter-iqd {filter}" if filter else ""
 
 

diff --git a/config/h5n1-cattle-outbreak.yaml b/config/h5n1-cattle-outbreak.yaml
@@ -75,6 +75,8 @@ refine:
   coalescent: const
   date_inference: marginal
 
+  genome_clock_filter_iqd:
+    FALLBACK: 3
   clock_filter_iqd:
     FALLBACK: false
 

diff --git a/ingest/build-configs/ncbi/defaults/host-map.tsv b/ingest/build-configs/ncbi/defaults/host-map.tsv
@@ -92,3 +92,6 @@ western sandpiper	Avian
 Wild-Bird	Avian
 EMU	Avian
 Emu	Avian
+Dromaius novaehollandiae	Avian
+White-winged Dove	Avian
+Rock Pigeon	Avian