If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Call mitochondrial chromosome (mitochondrial sequence) from whole genome sequence
I wonder if there is any commands purposely for mitochondrial sequence calling. I do have a whole genome sequence (in .bam), but now I want to call only the mitochondrial part of the sequence. Is it possible? Is there any command respective to it?
Also, is it possible for me to call the single nucleotide polymorphisms (SNPs) that located in mitochondrial part? Do I have to use commands for that also?
I am glad to hear from you guys. Anyway, thank you in advance!