Dear syednajeebashraf

You could find our resource mit-o-matic which can handle NGS datasets for Haplogroup analysis

If you attempt to haplotype your sequences through Mitomaster, please use the web service.

For a local run you might want to look at Phy-mer.

I have sequenced the human Mt genome from off target exome sequencing reads using the method of:

Picardi E, Pesole G. Mitochondrial genomes gleaned from human whole-exome sequencing. Nat Methods. 2012;9(6):523-4.

I then used the resulting consensus Mt DNA sequence (in fasta format) to determine the haplogroup using a local installation of Mitotool.