Mt DNA haplogroup analysis from HTS data

Question

[always_learning]

Hello Everyone!

Happy New year to one and all!

Could you please point me to some good tutorials/link/article/blog for Mt DNA haplogroup analysis?

Thanks
Najeeb

Answer 1

[Vinod Scaria]

Dear syednajeebashraf

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

Answer 2

[Jeremy Leipzig]

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.

Answer 3

[rbagnall]

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.