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jfnavarro · Nov 2, 2020 · 6f770f3 · 6f770f3
1 parent b43cb93
commit 6f770f3
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/hlapipeline/common.py b/hlapipeline/common.py
@@ -81,6 +81,6 @@ def annotate_variants(input, output, db, version, threads):
     :param threads: the number of threads to use
     """
     annovardb = '{} -buildver {}'.format(os.path.join(ANNOVAR_PATH, db), version)
-    cmd = '{} {} {} -thread {} -out output -vcfinput -remove -protocol {}'.format(
+    cmd = '{} {} {} -thread {} -out {} -vcfinput -remove -protocol {}'.format(
         os.path.join(ANNOVAR_PATH, 'table_annovar.pl'), annovardb, input, threads, output, ANNOVAR_ANNO)
     exec_command(cmd)