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So sorry to hear of your parents' passing.
Yes, your parents' return may list married filing jointly. The 2016 return should list your mother's death, with your father still alive. Your father's final return will be filed next year for the 2017 tax year. His filing status would be single (or qualifying widower if he had dependent children) and you should report his death on that return.
To report your mother's death, scroll to the very bottom of the page headed Your spouse's personal info. When you click Yes to My spouse passed away before filing this return, you will then be asked to type in the date of her death. (Click on the screen shot below.)
If you have followed these instructions, then all should be well, and you should see "Deceased" printed at the top of the form.
Before you file a decedent's return:
If you are filing both your return and your parents' in TurboTax, you will need to create another account in order to file another return. You can see the instructions in the TurboTax FAQ below to do so:
https://ttlc.intuit.com/replies/3288574
This article explains more about dealing with a death in the family.
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