Human Mitochondrial Variants Annotation

Question

[mks002]

Can anyone suggest some tool which can be used for Human Mitochondrial variants annotation?

I tried PROVEAN but I think it doesn't work for human Mitochondria.

Answer 1

[rbagnall]

Try Mitomaster. Select the SNV Query tab and enter variants as shown in the examples on the right hand panel.

Answer 2

[Gabriel R.]

I am not sure what you mean by annotation but have you tried Haplogrep2?

https://haplogrep.uibk.ac.at/

You can upload your fasta and you get variants from the rCRS and haplogroup assignments.

[mks002]

For the Human mitochondrial sample, i had done the annotation of the variants using SnpEff. From SnpEff I got the syn and non-syn information.

Still, I wanted to know what would the effect of these variations in some pathways.