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The tax withheld by Vanguard was only an estimated amount---just like when you have an employer withhold tax from your paychecks. When you enter your 1099R and combine all of the income from Vanguard with your other income from W-2's, etc., the software will use all of the income and all of the tax withheld from those sources of income, and calculate whether you owe more tax due or get a refund.
To enter your retirement income, Go to Federal> Wages and Income>Retirement Plans and Social Security>IRA 401 k) Pension Plan Withdrawals to enter your 1099R.
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