Because you are here on a F-1 Visa, you are required to file a FORM 1040-NR - U.S. Nonresident Alien Income Tax Return. You do not file this form with the Married Filing Jointly filing status, The form is for a an individual. That is why you were asked to indicate on the Form W-4 as Single.
The treaty that you are under the treaty between the United States and India in ARTICLE 21 Payments Received by Students and Apprentices. See Treaty between U.S. and India.
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