diff --git a/pkgs/applications/science/biology/manta/default.nix b/pkgs/applications/science/biology/manta/default.nix
new file mode 100644
index 000000000000..f0f0575e055a
--- /dev/null
+++ b/pkgs/applications/science/biology/manta/default.nix
@@ -0,0 +1,35 @@
+{ stdenv, fetchFromGitHub, cmake, zlib, python2 }:
+
+stdenv.mkDerivation rec {
+  pname = "manta";
+  version = "1.6.0";
+
+  src = fetchFromGitHub {
+    owner = "Illumina";
+    repo = "manta";
+    rev = "v${version}";
+    sha256 = "1711xkcw8rpw9xv3bbm7v1aryjz4r341rkq5255192dg38sgq7w2";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib python2 ];
+  postFixup = ''
+    sed -i 's|/usr/bin/env python2|${python2.interpreter}|' $out/lib/python/makeRunScript.py
+    sed -i 's|/usr/bin/env python|${python2.interpreter}|' $out/lib/python/pyflow/pyflow.py
+    sed -i 's|/bin/bash|${stdenv.shell}|' $out/lib/python/pyflow/pyflowTaskWrapper.py
+  '';
+  doInstallCheck = true;
+  installCheckPhase = ''
+    rm $out/lib/python/**/*.pyc
+    PYTHONPATH=$out/lib/python:$PYTHONPATH python -c 'import makeRunScript'
+    PYTHONPATH=$out/lib/python/pyflow:$PYTHONPATH python -c 'import pyflowTaskWrapper; import pyflow'
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Structural variant caller";
+    license = licenses.gpl3;
+    homepage = "https://github.com/Illumina/manta";
+    maintainers = with maintainers; [ jbedo ];
+    platforms =  platforms.x86_64;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 59492df5236a..fed4a37a88f7 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -23907,6 +23907,8 @@ in
 
   niftyseg = callPackage ../applications/science/biology/niftyseg { };
 
+  manta = callPackage ../applications/science/biology/manta { };
+
   octopus-caller = callPackage ../applications/science/biology/octopus { };
 
   paml = callPackage ../applications/science/biology/paml { };