How to call mitochondrial SNP?

Question

[hxlei613]

Hello. I have searched this question on biostars already.But I am not satisfied with the result. MitoSeek need a control to call mutation.Well I dont have a control. I have seen many papers said they used GATK but they didnt clearify UnifiedGenotyper or HaplotypeCaller. I also see someone try to use MuTect2. Also samtools can do this, but what's the parameter ? Can we treat mitochondrial as usual ? So far are there some specific precessures to call mtDNA SNP ? Thank you very much for comments.

Answer 1

[Jeremy Leipzig]

I take it you have aligned your sequences to rCRS and you have a .bam file? You can submit that to Haplogrep. You can also call the consensus sequence using samtools, which will yield a fasta you can submit to Mitomaster.

Samtools consensus sequence

Answer 2

[devenvyas]

This may not be as helpful, but have you tried to use Mapping-Iterative-Assembler, you can just assemble whole mitochondrial genomes and then align to the rCRS and call SNPs that way

Answer 3

[sriram_pharm]

Hi! recently I tried exploring some of latest variant callers which do a decent job. 1) Mutserve and 2) Google-DeepVariant (PEPPER DV). Anybody who have used these pipelines please share your experiences.

[Ram]

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