(I'm leaving off the discussion about the "we call" portion of the phrase, as that has been quite suitably addressed in other answers.)
BS can also stand for "baloney sandwich".
Baloney is a word that can be used to refer to something that is false. If someone speaks something untrue, whether from dishonesty or simply error, then that a person could exclaim, "Baloney!".
If someone says something that has a bit of untruth, a person could refer to smelling a bit of baloney in what is being heard. However, if you have a giant whopper of a tale, you could have so much baloney that you have enough to make a decent-sized sandwich out of it. Therefore, a bunch of lies may be referred to as a "baloney sandwich".
This phrasing has seen less usage as widespread profanity has simply become more popular, but if you're interested in keeping language clean of inappropriate language, then BS can refer to "baloney sandwich".
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There is a card game called BS in which you literally call out "BS" when you think someone is lying. I'm sure the game came from the phrase (not the other way around), but it's what I and many others think of when the phrase "call BS" is used.
– BlueRaja - Danny Pflughoeft – 2018-02-18T19:28:52.0536@BlueRaja-DannyPflughoeft I actually suspect that the phrase "call BS" may have come from the game, which of course took its name from the latter expression. – chrylis -cautiouslyoptimistic- – 2018-02-19T02:36:47.090
2@BlueRaja-DannyPflughoeft We should post an [English.SE] question asking about the origin. – jpmc26 – 2018-02-19T05:45:56.907
4@BlueRaja-DannyPflughoeft Surely people were calling, "bullshit!" before the game, but the specific term "to call bullshit" has indications of being spawned from the game. In typical use otherwise, the word "call" would be a bit awkward IMO. Since the game has solidifed that terminology, though, it has become ubiquitous to use the entire phrase. – Darren Ringer – 2018-02-19T14:47:03.617
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There is now a course at the University of Washington called "Calling Bullshit". The goal of the course "is to help students navigate the bullshit-rich modern environment by identifying bullshit, seeing through it, and combating it with effective analysis and argument."
– eipi10 – 2018-02-19T22:42:36.8701You might also see someone saying, "I call shenanigans!" with essentially the same meaning. – Todd Wilcox – 2018-02-20T02:47:23.400
Calling bs was around since the 70s at least, probably a lot longer. I am pretty sure it pre-dated the card game. – Bill K – 2018-02-21T20:56:05.540
@BillK - "BS" itself is certainly way older. "I call BS" I don't believe I heard before the very late 1990's (on Slashdot). I remember thinking it looked very ungramattical to my AmE eyes. But it slowly caught on. Prior to that "BS" was mostly just used as a single-word imperative sentence. So the timing is probably consistent with that phrase coming from the card game. – T.E.D. – 2018-02-21T21:43:10.710