There are several electron apps available to use whatsapp in a standalone window. The main advantage of using such app is, it will provide native notifications. Try following apps. Linux 64x version available.
http://rambox.pro/(Download AppImage 64 Bit)
http://meetfranz.com/#download_all(Download Linux 64 bit. Unpack and run)
https://github.com/bcalik/Whatsapp-Desktop(Download Linux 64 bit. Unpack and run)