Question: Calling chrMT only from BAM
0
gravatar for igorm
4 months ago by
igorm10
igorm10 wrote:

Hi,

Is there a straight forward way to call variants from aligned BAM file only for the mitochondrial chromosome?

Thanks

mt assembly variant calling • 156 views
ADD COMMENTlink modified 11 weeks ago • written 4 months ago by igorm10
1

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.

ADD REPLYlink modified 4 months ago • written 4 months ago by ATpoint36k
1
gravatar for igorm
11 weeks ago by
igorm10
igorm10 wrote:

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.

samtools --version
samtools 1.7

bcftools --version
bcftools 1.7
ADD COMMENTlink written 11 weeks ago by igorm10
1
gravatar for Gabriel R.
4 months ago by
Gabriel R.2.7k
Danmarks Tekniske Universitet
Gabriel R.2.7k wrote:

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.

ADD COMMENTlink modified 4 months ago • written 4 months ago by Gabriel R.2.7k

I guess you have some autocorrect running that changes mitochondrial into modern?

ADD REPLYlink modified 4 months ago • written 4 months ago by ATpoint36k
1

I have editted my post with "mitochondrial modern" and "mitochondrial ancient" to make it clear that I mean mitochondrial. Apologies for the confusion!

ADD REPLYlink written 4 months ago by Gabriel R.2.7k
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