Is there a straight forward way to call variants from aligned BAM file only for the mitochondrial chromosome?
Sure, tell the variant caller to only consider that chromosome. For more information, please read the manual of the variant caller. Most variant callers have suh options.
I ended up using samtools and bcftools like so:
samtools mpileup -uf human_g1k_v37.fasta sample.bam --region MT | bcftools call -m --ploidy 1 > sample_mt_only.vcf
This puts the entire MT in vcf. If I would supply "-v" parameter to bcftools, it would only store the variants.
We published a caller for mitochondrial ancient DNA but it is suitable for mitochondrial modern DNA as well. For mitochondrial modern DNA the problem is even simpler. The name of the program is endoCaller part of the (schmutzi package)
You can call it as such:
endoCaller -seq consensus.fa -log consensus.log -name [name sample here] chrMT.fa inputMT.bam
You might want to use the option -qual, this will filter bases according to a PHRED scale. e.g. -qual 50 means the confidence will be 1/100,000.
I guess you have some autocorrect running that changes mitochondrial into modern?
I have editted my post with "mitochondrial modern" and "mitochondrial ancient" to make it clear that I mean mitochondrial. Apologies for the confusion!
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