The cost basis on the Form 1099-B should be entered as it is reported on the form. That amount should then be adjusted, by entering your "Adjusted Cost Basis" on the applicable screen in the program. If this screen isn't available, you may not have indicated the transaction was for Employee Stock - ISOs. This could be due to importing the transactions. I have found that the best way to report sales of company stock is to manually input each transaction as opposed to importing them. If you do it this way, the program will guide you through adjusting your cost basis.
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