I'm doing the exact same thing, although with my own genome. Things I have done - Annotate the variants with its frequency. You can do that with Ensembl. There

I'm doing the exact same thing, although with my own genome. Things I have done - Annotate the variants with its frequency. You can do that with Ensembl. There's an official Docker image on their website that I suggest you use. You will have to run "./INSTALL.pl" to download some files (they call them caches) and then "vep -i /genome.vcf --af --max_af --af_1kg --af_esp --af_gnomad -o genome_with_freqs.vcf --cache". - If you know a specific region of the genome you want to look at, you can use tabix to extract all the variants in it. For example: "tabix genome.vcf.gz chr16:82,624,969-83,802,640 > cdh13_variants" will extract all the variants in that specific region. - Use igv to browse the variants visually. In general, the tools you will come across aren't very intuitive and its CLI interfaces aren't good. Prepare to spend a decent amount of time to make sense of everything. Honestly, if you know of a family member of her who happens to have similar symptoms, I would say the best thing you could do is to sequence that genome and see where they overlap. In any case, read some studies, find the loci where the variants cause problems, and then extract the variants. EDIT: On this last point: the cool thing about igv is that you can open vcf files and see only the variants; you can search for variants ("rs123456" in the search field) and it will show the variant and its surroundings; you can search for "chr16:82,624,969-83,802,640" and it will limit what's visible to that region; you can search for a gene and the search field will show you the region of the genome that the gene spans, which you can use for tabix later. You will often see in studies something like "variants in loci p13.12 of chromosome 16 were shown to have an effect in...". Right below the search bar you can see all those locis (p13.3, p13.2, etc.). Good luck! If you add your email in your profile, I will contact you.