If you have received a 1099-MISC with an entry in box 7, then you are self-employed. Your company is paying you as a contractor. The IRS will not allow you to file otherwise.
This is good for you in one way, and bad in another. As a contractor, you get to deduct every dime you spent on supplies, travel, etc. If you were an employee, you would only be able to deduct the amounts you spent that exceeded 2% of your income, and then only if your other deductible expenses exceeded the standard deduction.
The bad part is that you will have to pay the employer's share of payroll taxes (Medicare and Social Security). It also means that no tax was withheld from your income, so in addition to paying income tax, you will owe payroll tax.
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