In order to get the certificate into a usable format, the following java code was used.
InputStream inputStream = null;
X509Certificate appleRootCertificate = null;
try {
InputStream in = new FileInputStream(new File("/Users/mrezentes/Documents/workspace/AndroidPay/src/AppleRootCA-G3.cer"));
CertificateFactory certificateFactory = CertificateFactory.getInstance(X_509);
appleRootCertificate = (X509Certificate) certificateFactory.generateCertificate(in);
PEMWriter pw = new PEMWriter(new PrintWriter(System.out));
pw.writeObject(appleRootCertificate);
pw.flush();
pw.close();
}