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My Macbook Pro (Mid 2012) got its HDD corrupted due to some hardware issue. The issue has been fixed, however the MacBook lost its system partition data. The recovery partition is still there, but due to some issues (Read here), it never got upgraded to El Capitan's Recovery HD. Thus if I want to download the OS from Recovery Mode, it is installing Yosemite in it.

Is there any way I can reformat the MacBook and clean install El Capitan without first downloading Yosemite, installing it and then upgrading. I don't have any other Mac, but I do have a Windows Desktop. How can I possibly download and clean install El Capitan?

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    If you are close to an Apple Store, you can take it in and they are more than happy to install the OS for you. The one here had USB installers that the Geniuses used. – Allan Aug 22 '16 at 10:11
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The short answer is no. Without a different Mac you cannot download an El Capitan installer without first installing Yosemite on your Mac.

One way to do a clean install of El Capitan when only having one Mac and a Yosemite recovery partition is this:

  1. Install Yosemite using the recovery partition.
  2. Go to the App Store and download El Capitan.
  3. Use createinstallmedia to create a USB installation of El Capitan.
  4. Then you can use that usb media to format and do a clean install of your Mac.

Optionally you could skip the usb installation steps all together and install El Capitan, let it upgrade the recovery partition for you and use the fresh recovery partition to format and reinstall El Capitan as a freshly installed OS.

Instructions on how to use createinstallmedia can be found here: https://support.apple.com/en-us/HT201372

As a side note, have you tried if Internet recovery has a different version of the system compared to your local harddrive recovery. Hold Option-Command-R to start up from OS X Internet Recovery. As found here: https://support.apple.com/en-us/HT201314

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