Querying and viewing mitochondrial variants in IGV

[anjalijain22]

Hello,

Hope you're doing well! I am using the Hail backend of seqr and had a couple of questions regarding mitochondrial variants. My loaded dataset is an exome and uses the GRCh37 reference:

1. How do I query mitochondrial variants using variant lookup? Is the below error message to be expected?

2. I am unable to view the MT variants in IGV. The only option that I see is chrM- I suspect this is because of the reference genome that IGV is using. How can I change the reference for IGV to ensure I can correctly view mitochondrial variants?

Many thanks in advance for your help with this!

[hanars]

Hi Anjali, seqr does not support loading mitochondrial data from a regular VCF joint called with other chromosomes. Instead it requires that you use a mito-specific calling and annotation pipeline that accurately reflects homoplasmy/heteroplasmy levels and uses meaningful annotations. This pipeline is not currently available for local installations, we are hopeful that support will be added next year

[anjalijain22]

Ah I see! Thanks for your prompt response on this!