diff --git a/ivy.xml b/ivy.xml
index 96c1de844..ee24bc367 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -76,7 +76,7 @@
     <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />
 
     <!-- snpEff annotator for pipelines -->
-    <dependency org="net.sf.snpeff" name="snpeff" rev="2.0.2" />
+    <dependency org="net.sf.snpeff" name="snpeff" rev="2.0.4rc3" />
 
     <!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
     <exclude org="javax.servlet" />
diff --git a/settings/repository/net.sf.snpeff/snpeff-2.0.2.jar b/settings/repository/net.sf.snpeff/snpeff-2.0.4rc3.jar
old mode 100755
new mode 100644
similarity index 88%
rename from settings/repository/net.sf.snpeff/snpeff-2.0.2.jar
rename to settings/repository/net.sf.snpeff/snpeff-2.0.4rc3.jar
index bfd06f97f..ee5d02367
Binary files a/settings/repository/net.sf.snpeff/snpeff-2.0.2.jar and b/settings/repository/net.sf.snpeff/snpeff-2.0.4rc3.jar differ
diff --git a/settings/repository/net.sf.snpeff/snpeff-2.0.2.xml b/settings/repository/net.sf.snpeff/snpeff-2.0.4rc3.xml
similarity index 77%
rename from settings/repository/net.sf.snpeff/snpeff-2.0.2.xml
rename to settings/repository/net.sf.snpeff/snpeff-2.0.4rc3.xml
index f0568def4..5417641d3 100644
--- a/settings/repository/net.sf.snpeff/snpeff-2.0.2.xml
+++ b/settings/repository/net.sf.snpeff/snpeff-2.0.4rc3.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf.snpeff" module="snpeff" revision="2.0.2" status="release" />
+    <info organisation="net.sf.snpeff" module="snpeff" revision="2.0.4rc3" status="release" />
 </ivy-module>