Income tax return without form-16

One of my friend is working in an NGO (non-profit organization ) firm here in India. The company has affiliation with US based NGO. She recevied monthly pay in the form of NEFT payment and her employer so far didn't file TDS deduction in her monthly salary even though its above taxable slab. In the absence of her employer filing TDS and providing Form-16 to her, how do she files IT Return for FY 2014-15.

Is Bank NEFT transaction of higher value (greter than 50K and less than 100K )comes under income tax radar?

Thanks in Advanced.