I believe you would file - married filing jointly or married filing separately. If you file jointly, he would also sign the return. If you file married filing separately - he would not need to file as he does not meet minimum income threshold
If you use a tax preparer they can advise your properly as what the best option for you is, and also the IRS has a toll free number, you can always call them directly and ask questions of this nature. Good luck.
You may qualify for head of household if your husband was not a member of your household for the last six months of the year. There are some special rules where incarceration is considered a temporary absence but your case appears to be different than that. If you can qualify for HOH you may qualify for some tax credits that are not available for married filing separate. You should discuss this with a tax attorney or tax CPA.
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