Skip sites with unknown ref

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index e38f1ca5ef660eca6aa223d4ab4cfbd359408a2f..3c962eccb5f52b54628090a4d6f47025b39e1f54 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -246,6 +246,7 @@ Note: Some of the filters rely on annotations generated by SAMtools\/BCFtools.
          print; next;
        }
        next if ($t[4] eq '.'); # skip non-var sites
+    next if ($t[3] eq 'N'); # skip sites with unknown ref ('N')
        # check if the site is a SNP
        my $type = 1; # SNP
        if (length($t[3]) > 1) {