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Stacking software you set up to debayer with the correct pattern as required (RGGB) and certainly in Astro Pixel processor (Paid) it debayers individual subs when set to and you can save the individual subs in debayered form if you want. I know Deep Sky Stacker (Free) can debayer when stacking but I can't recall for individual sub preview.
There is also FITS Liberator and ASTAP which can be set up to debayer for examining subs.
Really all those programs are doing is something similar to the debayering that is done in camera when you are using a DSLR, but you don't generally want to debayer and re save the images from an OSC astro camera as colour before stacking. The best bet is to preview them debayered if you want but do whatever calibration with darks, bias, flats you need to and stack them from the raw state. I understand programs like Astro Pixel Processor do the calibration before debayering if you are using an OSC camera.
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