Hey pig.
I don't know if this is the right answer but I would imagine that if you are a share trader for tax purposes you would claim brokerage as an expense and then also account for GST in your business activity statement (BAS) if you are registered for GST.
Because I and my SMSF are investors (like most people) and subject to capital gains tax and am not registered for GST the brokerage is included in the cost base and the receipt of sales. That is, the brokerage (inclusive of GST) when purchasing shares is added to the cost base and the brokerage (inclusive of GST) when selling the shares is deducted to arrive at the net proceeds of the sale.
In summary for most investors selling shares is a capital gains tax event and brokerage is accounted for in the cost base and disposal proceeds of the CGT event inclusive of GST. For professional traders brokerage is an expense and if the trader is registered for GST then GST would be accounted for in the BAS.
I'm no expert so I don't know if there is a choice as to whether you claim the brokerage as a deduction or account for it in the CGT event as I do - but my accountant seems happy enough with my bookwork.
I know of someone who's SMSF is registered for GST but I think, according to my limited understanding of tax law, that is a bit questionable and I wouldn't try it on (nor would it be worth my time).