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I am abit confused with the ally rules in the WH codex. I would like to make an army which included both GK and SoB (most likely with a sisters parent list). Is it possible to use inducted guard in this, or does my use of GKs void my inducted guard option?

While I don't believe that Sisters and GK can be in the same army, but yes, you could use Inducted IG in the list.

Inducted guard is indeed fine with both. You could also have allied guard if you'd like.
I don't know of any problem mixing GKs and Sisters, but come to think on it I am the only serious Sisters player in my area, so maybe it just never came up. In so far as I know though, GKs do not count as "space marines" and as such do not violate the rules about mixing boys and girls.