modified: cre.vt.decompose.sh

naumenko-sa · Oct 24, 2018 · 86ac869 · 86ac869
1 parent 8328f1c
commit 86ac869
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/cre.vt.decompose.sh b/cre.vt.decompose.sh
@@ -11,6 +11,6 @@ bname=`basename $1 .vcf.gz`
 #already fixed in the new version
 #cat $bname.vcf | sed s/"##FORMAT=<ID=AD,Number=."/"##FORMAT=<ID=AD,Number=R"/ > $bname.modified.vcf
 
-vt decompose -s $1 | vt normalize -r ~/work/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa - | vt uniq - -o $bname.decomposed.vcf.gz
+vt decompose -s $1 | vt normalize -r ~/work/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -n - | vt uniq - -o $bname.decomposed.vcf.gz
 
 tabix $bname.decomposed.vcf.gz