IANAA, but you file a gigantic "Schedule-D". I have never done it with crypto, but there is standard software to do it for non crypto stuff.

I used GainsKeeper: http://www.wolterskluwerfs.com/tax-reporting/solutions/gains...

I see they do crypto, but I've never used it for that.

For companies, they have entire departments that consolidate trades and construct massive Schedule Ds