100%. remaking without up/down stream

mk150.sh

@@ -76,7 +76,7 @@ for gff in ~/tomato150/reseq/mapped/Heinz/*.vcf.gz; do
 		cd 150/$bn;
 		echo $PWD;
 
-		java -Xmx20g -jar $P/snpEff.jar -c $P/snpEff.config Slyc2.40 -v $gff >$bn.snpeff.vcf 2>log.log;
+		java -Xmx20g -jar $P/snpEff.jar eff -no-upstream -no-downstream -c $P/snpEff.config Slyc2.40 -v $gff >$bn.snpeff.vcf 2>log.log;
 	fi
 
 	cd $P;