Tool for identifying mitochondrial SNP from exome seq data

Question

[peris]

I have sequenced 35 of familial exome samples spread over 15 families. I want to study the mitochondrial SNPs on these samples. I have checked in the aligned file and there exist off target mitochondria capture. Is there any tool for identifying mitochondrial SNPs from exome seq bam file?

Answer 1

[GouthamAtla]

Aligning the reads to mitochondria sequence would not help ? You can download the mitochondria DNA from here. http://www.mtdb.igp.uu.se

If you have BAM file, you can extract the reads that mapped top "MT" sequences and call SNPs. If the "MT" is not included in the genome that is been used for alignment, you can extract th unmapped reads and align them to MT sequences and call SNPs.

[Brian Bushnell]

I think he's looking for a variant caller. I suggest you try samtools mpileup, or GATK; both are designed for finding variants in bam files.