I bought APP recently and decided it would smooth processing out to use fits files instead of native raw files. I've been using DNG which says the CFA pattern is "BGGR" but now I find that the fits header says its "RGGB".

Attached are a DNG and FITS captured from the same Pentax K-5II.

Édit : this is a bad setting in Ekos control panel. CFA type must be set manually.