--- scripts/snpSift.orig	2021-04-19 15:55:06 UTC
+++ scripts/snpSift
@@ -13,9 +13,9 @@
 # Created by: Brad Chapman
 #---------------------------------------------------------------------------------------------------
 
-jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)"
+jardir=%%JAVAJARDIR%%/snpeff
+JAVA_HOME=%%JAVA_HOME%%
 
-java=java
 if [ -e "$JAVA_HOME/bin/java" ]
 then
 	java="$JAVA_HOME/bin/java"
@@ -44,4 +44,3 @@ if [ "$jvm_mem_opts" == "" ]; then
 fi
 
 exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/SnpSift.jar $pass_args
-exit