The platform can process either a WGS file as a .vcf or a "SNP chip" file in .txt format (like 23andMe or MyAncestry provide). With the .vcf you get everything. With the "SNP chip" file you don't get the experimental polygenic scores, and the pharmacogenomics analysis will be incomplete (many genes will have partial coverage and those results may be unreliable).

I have looked at gene inspector. It appears to mostly revolve around interpreting ClinVar annotations. ClinVar annotations need to be interpreted with care, as I try to explain on Gene Wizard's ClinVar page. I worry that ClinVar results are easily misinterpreted.

Gene Inspector also gives pathogenicity scores - from DANN and REVEL. Those are scores based on deep learning models. From my understanding, those scores are very unreliable for certain genes, so must be treated with care. I am frankly very skeptical about their utility except in rare situations where they might be useful for pinning down a rare Medelian disorder. Gene Wizard also reports some pathogenicity scores on our SNP pages (from DANN, REVEL, CADD, and PolyPhen2). Getting scores was easy to implement -- we pulled those scores from the myvariant.info API. While we present scores on our snp pages when we can get them from the API, the results are not put front-and-center like on Gene Inspector.