Human Mitochondrial Variants Annotation
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5.0 years ago
mks002 ▴ 220

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.

Assembly sequencing SNP alignment • 2.3k views
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5.0 years ago
rbagnall ★ 1.7k

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

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5.0 years ago
Gabriel R. ★ 2.8k

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.

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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.

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