The lender cannot determine how you are paid, either as an independent contractor versus an employee. If you are issued a 1099-MISC, then you are considered self-employed and must file a Schedule C. Self-employment income can be considered for lending purposes, but they generally want to see two years worth of income to determine your average.
There are certain IRS restrictions on when you can be a W-2 employee versus an independent contractor issued a 1099-MISC. See the link below for more information:
Independent Contractor or Employee
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