diff --git a/pkgs/applications/science/biology/vcftools/default.nix b/pkgs/applications/science/biology/vcftools/default.nix
new file mode 100755
index 00000000000..ab3050955df
--- /dev/null
+++ b/pkgs/applications/science/biology/vcftools/default.nix
@@ -0,0 +1,24 @@
+{ stdenv, fetchFromGitHub, htslib, zlib, autoreconfHook, pkgconfig, perl }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "vcftools";
+  version = "0.1.15";
+
+  src = fetchFromGitHub {
+    repo = pname;
+    owner = "vcftools";
+    rev = "v${version}";
+    sha256 = "15yxr4kidqb42gkbd6rjra6b07wpl6rgivlh9q73yavh5myafqk4";
+  };
+
+  buildInputs = [ autoreconfHook pkgconfig zlib perl ];
+
+  meta = with stdenv.lib; {
+    description = "A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project";
+    license = licenses.lgpl3;
+    platforms = platforms.linux;
+    homepage = https://vcftools.github.io/index.html;
+    maintainers = [ maintainers.rybern ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 4e70061eb03..179e8a46a35 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -4860,6 +4860,8 @@ with pkgs;
 
   vboot_reference = callPackage ../tools/system/vboot_reference { };
 
+  vcftools = callPackage ../applications/science/biology/vcftools { };
+
   vcsh = callPackage ../applications/version-management/vcsh {
     inherit (perlPackages) ShellCommand TestMost;
   };