diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix
new file mode 100644
index 00000000000000..d4e4ed5b954fde
--- /dev/null
+++ b/pkgs/applications/science/biology/bcftools/default.nix
@@ -0,0 +1,26 @@
+{ stdenv, fetchurl, zlib, htslib }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "bcftools";
+  version = "1.3.1";
+
+  src = fetchurl {
+    url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2";
+    sha256 = "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj";
+  };
+
+  buildInputs = [ zlib ];
+
+  preBuild = ''
+    makeFlagsArray=("HSTDIR=${htslib}" "prefix=$out")
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants";
+    license = licenses.mit;
+    homepage = http://www.htslib.org/;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.mimadrid ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 79718fc79e5b75..11c0641558b1af 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15883,6 +15883,8 @@ in
     stdenv = overrideCC stdenv gcc49;
   };
 
+  bcftools = callPackage ../applications/science/biology/bcftools { };
+
   emboss = callPackage ../applications/science/biology/emboss { };
 
   htslib = callPackage ../development/libraries/science/biology/htslib { };