diff --git a/modules/local/bcftools.nf b/modules/local/bcftools.nf
index 8f61b9f..5290222 100644
--- a/modules/local/bcftools.nf
+++ b/modules/local/bcftools.nf
@@ -70,6 +70,7 @@ process BCF_FILTER {
   bcftools_filt_vcf = "${prefix}.bcftools_filt.vcf"
   """
   bcftools norm \\
+    --check-ref w \\
     -Ov \\
     -m- \\
     -f $fasta \\
diff --git a/modules/local/clair3.nf b/modules/local/clair3.nf
index b431a5c..d19edeb 100644
--- a/modules/local/clair3.nf
+++ b/modules/local/clair3.nf
@@ -54,6 +54,7 @@ process CLAIR3 {
       --output=${clair3_dir} \\
       --haploid_sensitive \\
       --enable_long_indel \\
+      --keep_iupac_bases \\
       --fast_mode \\
       --include_all_ctgs