How to call mitochondrial SNP?
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7.0 years ago
hxlei613 ▴ 100

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.

SNP mitochondrial • 2.3k views
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7.0 years ago

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

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7.0 years ago
devenvyas ▴ 740

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

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5 weeks ago

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.

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