Depth of Coverage in Mitochondrial Genome with Samtools

Question

[Lida]

Hi all

I want to ask you how to calculate mitochondrial genome's depth of coverage with samtools on linux ubuntu? I have done this work about some regions of chromosomes on BAM file with samtools, but those commands don't answer about mitochondrial genome.

Thanks

[Pierre Lindenbaum]

commands don't answer about mitochondrial genome

what does that mean ?

also check you're using the correct chromosome name (chrM instead of chrMT...)

[Lida]

I meant that those commands were not executed.

Yes, thank you. I tried this "chrM", but it gave me an error. In command to calculate the depth of coverage over the entire length of the mitochondrial genome, what regions should I type in the command after "chrM"?

[Pierre Lindenbaum]

I meant that those commands were not executed.

?

what is the command ?

[Lida]

The commands that I used to calculate the depth of coverage in different regions of different chromosomes did not work for the mitochondrial genome.

Is there a special command to calculate the depth of coverage of certain regions in mitochondrial genome?

[Pierre Lindenbaum]

that's what I asked : what is the command ?

[Lida]

The command was: samtools depth -a -H -r chr number:from-to -o FILE restored BAM file

Now my problem about mitochondrial genome is solved with this command: samtools depth -a -H -r MT:from-to -o restored BAM file

Thanks a lot for your help

[Darked89]

You may check first if the BAM file contains contigo corresponding to chrM/MT with or without the chr prefix. Like: samtools view -H bam_file | grep SQ

[Lida]

I did it. thank you for your help Now my problem about mitochondrial genome is solved with this command: samtools depth -a -H -r MT:from-to -o restored BAM file