diff --git a/config/h5n1-cattle-outbreak.yaml b/config/h5n1-cattle-outbreak.yaml
index 13f6505..629f413 100644
--- a/config/h5n1-cattle-outbreak.yaml
+++ b/config/h5n1-cattle-outbreak.yaml
@@ -69,6 +69,9 @@ filter:
   exclude_where:
     FALLBACK: host=laboratoryderived host=ferret host=unknown host=other host=host gisaid_clade=3C.2
 
+mask:
+  min_support: 0 # This lets all positions through regardless of how many sequences have a base
+
 
 refine:
   coalescent: const
diff --git a/config/h5n1-d1.1.yaml b/config/h5n1-d1.1.yaml
index fd4fcd4..7be2a54 100644
--- a/config/h5n1-d1.1.yaml
+++ b/config/h5n1-d1.1.yaml
@@ -61,6 +61,8 @@ filter:
   exclude_where:
     FALLBACK: host=laboratoryderived host=ferret host=unknown host=other host=host gisaid_clade=3C.2
 
+mask:
+  min_support: 50 # This masks any position where <50% of sequences have a base
 
 refine:
   coalescent: const
diff --git a/rules/cattle-flu.smk b/rules/cattle-flu.smk
index 5553277..f737b90 100644
--- a/rules/cattle-flu.smk
+++ b/rules/cattle-flu.smk
@@ -66,7 +66,7 @@ rule join_segments:
     input:
         alignment = expand("results/{{subtype}}/{{segment}}/{{time}}/aligned_{genome_seg}.fasta", genome_seg=SEGMENTS) 
     output:
-        alignment = "results/{subtype}/{segment}/{time}/aligned.fasta"
+        alignment = "results/{subtype}/{segment}/{time}/aligned_unmasked.fasta"
     wildcard_constraints:
         subtype = 'h5n1-cattle-outbreak|h5n1-d1.1',
         segment = 'genome',
@@ -78,6 +78,25 @@ rule join_segments:
             --output {output.alignment}
         """
 
+rule mask_genome:
+    input:
+        alignment = "results/{subtype}/{segment}/{time}/aligned_unmasked.fasta"
+    output:
+        alignment = "results/{subtype}/{segment}/{time}/aligned.fasta",
+    params:
+        percentage = config['mask']['min_support']
+    wildcard_constraints:
+        subtype = 'h5n1-cattle-outbreak|h5n1-d1.1',
+        segment = 'genome',
+        time = 'default',
+    shell:
+        r"""
+        python scripts/mask.py \
+            --alignment {input.alignment} \
+            --percentage {params.percentage} \
+            --output {output.alignment}
+        """
+
 rule genome_metadata:
     input:
         sequences = "results/{subtype}/{segment}/{time}/aligned.fasta",
diff --git a/scripts/mask.py b/scripts/mask.py
new file mode 100644
index 0000000..d5df8c2
--- /dev/null
+++ b/scripts/mask.py
@@ -0,0 +1,37 @@
+
+import argparse
+from augur.io.sequences import read_sequences, write_sequences
+from Bio.Seq import MutableSeq
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument('--alignment', type=str, required=True, help='genome alignment')
+    parser.add_argument('--percentage', type=str, required=True, help='positions with less coverage than this will be masked')
+    parser.add_argument('--output', type=str, required=True, help='masked genome alignment')
+
+    args = parser.parse_args()
+
+    # Store everything in memory
+    alignment = list(read_sequences(args.alignment))
+    genome_size = len(alignment[0].seq)
+    counts = [0 for _ in range(0, genome_size)] # zero-based
+    valid_bases = set(list("ATGCatcg"))
+    n_genomes = len(alignment)
+
+    for sample in alignment:
+        for idx, base in enumerate(sample.seq):
+            if base in valid_bases:
+                counts[idx] += 1
+
+    mask_bool = [c/n_genomes*100 < float(args.percentage) for c in counts]
+    mask_sites = [i for i,b in enumerate(mask_bool) if b==True]
+
+    print("Masking sites (zero-based):", mask_sites)
+    print("Total number of sites to mask:", len(mask_sites))
+
+    for sample in alignment:
+        sample.seq = MutableSeq(sample.seq)
+        for idx in mask_sites:
+            sample.seq[idx] = 'N'
+
+    write_sequences(alignment, args.output)
\ No newline at end of file