Many mortgage companies have different FICO score requirements for certain programs. Tax returns and 1099's are the documentation of income needed for a self-employed person. The income is reviewed for the prior two years. If you have been self-employed for less than two years, there could be a problem, but solutions are available. Many times a problem arises due to the different missions of a tax return vs. a mortgage application.
Most taxpayers attempt to minimize taxable income for tax purposes.
However, the mortgage loan is qualified based on income, so indicating a minimal taxable income can prevent you from qualifying for as much home as you would like. Commission and bonus income is averaged for the prior two years and that average is used for qualification purpose. Also it may be necessary to provide some evidence that continued bonus income is probable. You should consult a tax advisor regarding the deductibility of interest costs.