diff --git a/bcbio/variation/effects.py b/bcbio/variation/effects.py
index <HASH>..<HASH> 100644
--- a/bcbio/variation/effects.py
+++ b/bcbio/variation/effects.py
@@ -276,7 +276,7 @@ def get_db(data):
     snpeff_base_dir = None
     if snpeff_db:
         snpeff_base_dir = utils.get_in(data, ("reference", "snpeff"))
-        if not isinstance(snpeff_base_dir, basestring) and os.path.isdir(snpeff_base_dir):
+        if not (isinstance(snpeff_base_dir, basestring) and os.path.isdir(snpeff_base_dir)):
             snpeff_base_dir = utils.get_in(data, ("reference", "snpeff", snpeff_db))
         if not snpeff_base_dir:
             # We need to mask '.' characters for CWL/WDL processing, check for them here
effects: avoid lookup issues with non-CWL snpEff