modified: cre.vt.normalize.sh

naumenko-sa · Oct 24, 2018 · 8328f1c · 8328f1c
1 parent d6262d0
commit 8328f1c
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/cre.vt.normalize.sh b/cre.vt.normalize.sh
@@ -5,7 +5,9 @@
 #PBS -d .
 #PBS -l vmem=20g,mem=20g
 
+# do not fail if a variant in inconsistent with the reference
+
 bname=`basename $vcf .vcf.gz`
 
-vt normalize -r ~/work/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa $vcf | vt uniq - -o $bname.normalized.vcf.gz
+vt normalize -r ~/work/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa $vcf -n | vt uniq - -o $bname.normalized.vcf.gz
 tabix $bname.normalized.vcf.gz