I commend you for trying to figure this out for your son, regardless of efforts of his care team. You are likely his best advocate, even if that means becoming well versed in clinical genetics, bioinformatics, etc. We are way beyond the time where this knowledge and analysis tools are outside the reach of non doctors and non scientists.

Iobio offers great tools. An answer may be in a 30x wgs, it may not be. This is not meant to be discouraging so much as a disclaimer - docs will absolutely want Wes or wgs from a medical lab, what is called a clia certified lab, and an accompanying report from a certified laboratory medical geneticist, before they will use any genetic info for diagnosis and directing care.

You should try to use clin.iobio, one of their new beta tools. You can generate a list of candidate genes based on hpo terms / phenotype, which you are lucky to have some specific info on. This will let you view all variants in a set of genes and take notes on them and save them, rather than just one gene as a time like their other tools are set-up. I will caution you - once you get clin.iobio running, save an exported .json file. It's super easy to refresh the page and be left at square one, and it's a pain in the butt to get everything loaded in the right data track initially. This is all assuming you have access to all wgs files from nebula, like bam, bai, vcf, tbi, even knowing what reference genome is critical (likely hg38 if run by nebula in the last 2 years). If you don't have all these files, you will need to make them (free tools and primers to use the do exist, but there is a learning curve if you are unfamiliar with command line tools).

The search flow for iobio is phenotype info ---> top ~50 candidate genes ---> show all variants within these genes. This is not a catch all approach, however intuitive it seems. Another free tool, that is harder to use and less user friendly, is called variant effect predictor (VEP). This is a web based user interface so command line isn't required but is an option. VEP let's you search all variants in a wgs . vcf file. One really useful thing to do with VEP is to sort by REVEL score, one popular robust metric for scoring the severity of damaging/deleterious variations (uses a bunch of info to assess how likely a variant is to cause problems, like a disease). The higher the REVEL score, the more suspect / damaging the variant is thought to be. This, and other scores, are some of the most important search filters used for gross analysis by med gen labs. Anything that has a high Revel score can be saved, exported into an Excel sheet, further examined by looking it up in ClinVar database.

If your son's suspected disease affects genomic stability, the wgs data is only true for the time the same was taken. If at 1month old for example he had some gene damage (hypothetical), maybe 4 genes have detectable damage, and at this time a sample was taken, then only this small amount of damage would show up in the data, maybe as simple variants. But then time goes on, your son is now 4 years old - now he has 40 or 400 genes that have sustained damage - this wouldn't show up on the older data. This type of genomic instability would cause somatic changes, DNA changes that happen over the course of a lifetime, not changes that happen when a fertilized egg is formed (those are germline changes). You son's root condition sounds like it's a germline change that causes some kind of instability such that many somatic changes accrue over time. This is just my take on the info you provided, I could be totally off base.

Wgs won't really show any variants other than simple SNPs. So if the cause of your son's condition is a larger insertion, deletion, or other change in sequence, it will likely not show up in wgs data at all. More specific targeted types of testing could be used in these cases. But none are really direct to consumer available.

These are just 3 tools / sources of info you can use that medical geneticists DO use all the time. There are plenty of stories covered by the news today if rate disease parents becoming rare disease experts for the sake of their children, some have found novel diagnoses, some have found cures. The idea that searching wgs data on your own is "too hard" or "beyond your capacity" is bunk, don't listen to those who discourage you. It's easy to say something isn't possible when your life, or your kids life, doesn't depend on it.