I would like to preface this post by saying that I'm a biochemical geneticist by trade and primarily work with biochemical pathways and biomarker detection. I have zero coding experience and my limited molecular genetic experience is exclusively in variant curation.
I have a keen interest in mitochondrial disorders, so when the opportunity arose to work on a project to help establish my facility as a center for WGS anaylsis, I jumped on it (without really thinking!). I have a VCF file from NextGENeV2.4.1 (I'm currently working with this in excel) that does not contain mutations in the mitochondrial genome. I would like to manipulate the VCF file to include about a dozen or so common mitochondrial mutations to be annotated using Alissa 5.3.
Question: 1. Are there any resources available (I've found this: http://samtools.github.io/hts-specs/VCFv4.2.pdf) that can tell me what I'm looking at in the current VCF file and what it means? My biochemical brain only sees letters and numbers.... What data is critical to have to feed into Alissa? 2. Is Alissa the best platform to be using for mitochondrial genomes? If not, what are other suggestions?
I'm feeling very out of my depth here.