Hi and welcome to Just Answer!
As long as you are legally married - you may file a joint tax return if you both agree.
You may however file a separate tax return either as Married Filing separate (MFS) or as Head of Household (HOH) if you qualify.
To qualify for the HOH filing status - you should not live together with your spouse at least last six months of the year and have a qualified dependent living with you (your would qualify). You also need to provide more than haft of your household support.
If you do not feel comfortable to file a joint tax return - I suggest not to do so. Please be aware that if you do - you will be jointly liable for any tax liability resulted from that tax return.
However before you decide - I suggest to fill forms both ways and compare - it is possible that filing jointly will result in better refund, but there will be an issue how the refund will be divided - so you might want to an agreement before filing.
If you are using any tax preparation software - there should be an option to compare MFJ via MFS. If there is no difference or a difference is not substantial - you might better to file separately.
Please let me know if you need any help with estimations or any other clarification.