diff --git a/pkgs/applications/science/biology/snpeff/default.nix b/pkgs/applications/science/biology/snpeff/default.nix
new file mode 100644
index 000000000000..6c7a6b969ee6
--- /dev/null
+++ b/pkgs/applications/science/biology/snpeff/default.nix
@@ -0,0 +1,31 @@
+{stdenv, fetchurl, jre, unzip, makeWrapper}:
+
+stdenv.mkDerivation rec {
+  name = "snpeff-${version}";
+  version = "4.3i";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/project/snpeff/snpEff_latest_core.zip";
+    sha256 = "0i1slg201c8yjfr4wrg4xcgzwi0c8b9l3fb1i73fphq6q6zdblzb";
+  };
+
+  buildInputs = [ unzip jre makeWrapper ];
+
+  installPhase = ''
+    mkdir -p $out/libexec/snpeff
+    cp *.jar *.config $out/libexec/snpeff
+
+    mkdir -p $out/bin
+    makeWrapper ${jre}/bin/java $out/bin/snpeff --add-flags "-jar $out/libexec/snpeff/snpEff.jar"
+    makeWrapper ${jre}/bin/java $out/bin/snpsift --add-flags "-jar $out/libexec/snpeff/SnpSift.jar"
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Genetic variant annotation and effect prediction toolbox.";
+    license = licenses.lgpl3;
+    homepage = http://snpeff.sourceforge.net/;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.all;
+  };
+
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index d59650440477..97c8741d6fa6 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -17008,6 +17008,8 @@ with pkgs;
 
   samtools = callPackage ../applications/science/biology/samtools/default.nix { };
 
+  snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };
+
   varscan = callPackage ../applications/science/biology/varscan/default.nix { };
 
   bwa = callPackage ../applications/science/biology/bwa/default.nix { };