VAT is lavied on broker commission, not in the transaction amount please note that.
For below 50000 transaction you are charged 1% brokerage commision and above that you are charged 0.9% brokerge commission. With this VAT implementation you will be charged as below

For prevailing 1% brokerage commission provision.
1 % + 13% of 1% = 1.13% brokerage commission including VAT

For prevailing 0.9% brokerage commission provision
0.9% + 13% of 0.9% = 1.017%

So don't get mislead by the news. VAT will be lavied on Brokerage commission but not on the Transaction amount or the capital gain.