Question: How to call mitochondrial SNP?
2
gravatar for hxlei613
2.3 years ago by
hxlei61380
Bangladesh
hxlei61380 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 • 1.1k views
ADD COMMENTlink modified 2.3 years ago by devenvyas580 • written 2.3 years ago by hxlei61380
3
gravatar for Jeremy Leipzig
2.3 years ago by
Philadelphia, PA
Jeremy Leipzig18k 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 2.3 years ago • written 2.3 years ago by Jeremy Leipzig18k
0
gravatar for devenvyas
2.3 years ago by
devenvyas580
Stony Brook
devenvyas580 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 2.3 years ago by devenvyas580
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