Question: How to call mitochondrial SNP?
gravatar for hxlei613
3.2 years ago by
hxlei61390 wrote:

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 • 1.3k views
ADD COMMENTlink modified 3.2 years ago by devenvyas630 • written 3.2 years ago by hxlei61390
gravatar for Jeremy Leipzig
3.2 years ago by
Philadelphia, PA
Jeremy Leipzig19k wrote:

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

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Jeremy Leipzig19k
gravatar for devenvyas
3.2 years ago by
Stony Brook
devenvyas630 wrote:

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

ADD COMMENTlink written 3.2 years ago by devenvyas630
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