From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 19 Jan 2011 14:28:02 +0000 (+0000)
Subject: Skip sites with unknown ref
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=5a38c3f189830b809d1f83de68941c8924c0382b

Skip sites with unknown ref
---

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index e38f1ca..3c962ec 100755
--- 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) {