Which specific markers are you looking at?
Raspistill by default includes EXIF headers and a thumbnail. Disable the thumbnail by adding "-thumb none" to the commandline, and "-exif none" for the EXIF. And don't add the "-raw" option or you'll get a big block of the raw Bayer data appended to the JPEG data.
Software Engineer at Raspberry Pi Trading. Views expressed are still personal views.
I'm not interested in doing contracts for bespoke functionality - please don't ask.