I'm not quite sure what you mean!
Think about what CIS is - it is simply part of the builder's pay which isn't paid to him but is paid to HMRC for him, in respect of his personal tax liability.
So when working out VAT, don't make any deductions for CIS, just work with the figure from before the CIS deduction is made.
The builder's invoices would break down like this eg:
10 hours @ £10 per hour = £100 Plus VAT @ 20% = £20 Total invoice = £120
Less CIS @ 20% of pre VAT value = £20
Net amount to pay = £100
Looking at it the other way around:
If you know that the builder was paid £100 (that's the cash, cheque or whatever that he actually received) and a deduction for CIS was made of £20, then his invoice total was for £120.
The VAT amount is £120/6 ie. £20
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