I am Sanjay, I came to USA on July'06 and have my wife along with me.
I have H1B and my wife has H4.
I was in CA till Dec'06 I have my W2 in place.
My question is how should I file the tax.
By filing the state tax separately and by filing the 1040 or 1040NR for IRS.
How should I include my wife so that she can get TIN Number.

Please help me out as I am confused here.

You need to submit W-7 for ITIN for wife with your tax return. The process has been posted numerous times over the last month.

You or your wife must meet the Substantial Presence Test before you can file jointly. That means you must wait until May before you can file.

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