I have been in USA for about two and a half half years on F1 visa. In 2013 I was on at F1 and F1 OPT till 30 September 2013. After that I switch to H1B status. I am a nonresident alien for tax purposes. I am an Indian citizen. Am I eligible to claim US India tax treaty the benefits per Chapter 5 Pub 519 for 1040 NR (http://www.irs.gov/publications/p519/ch05.html)? The treaty would give me a standard deduction of $6100. I am not sure because its sites like sprintax on Glacier Tax Prep I not taking this into account then I am computing taxes using them. Is there a limit on the number of years for which I can claim treaty benefits?
There is a limit on how many years you can claim treaty benefits, and when you're on H1b - you're resident for tax purposes (except for the first year where you can usually choose not to be).
If you're a non-resident - you can always itemize, I do not know how "the treaty would give you an itemized deduction of $6100". What the Indo-US treaty may be able to give you in some cases is a standard (i.e.: not itemized) deduction, which is generally unavailable for non-residents.
Since you're specifically asking about the STANDARD deduction available to Indian students under the Indo-US treaty, then the answer for this specific question is NO. If for any part of the year you're in any status other than the one allowing the deduction under the treaty (i.e.: any status that is not F1/J1) - you cannot claim the standard deduction.
If you're a H1b filing as non-resident - you can only claim itemized deduction.