According to this study published recently in the Journal of the American College of Cardiology, whole genome testing may sometimes be used to identify the gene(s) responsible for HCM when targeted genetic testing (the type used in the clinical setting) has been inconclusive.
In particular, the study found the responsible gene(s) in 9 of 26 families (20%) in whom targeted testing had previously been inconclusive.
When used as the initial form of genetic testing, whole genome sequencing identified the responsible HCM gene in 5 of 12 families, or 42%.
According to this article in Wired U.K., a whole genome sequencing test costs about $600 and takes just a few weeks to complete. On the other had, the cost of data storage necessary to store such a large amount of collective data is, according to this article, prohibitively high.
If not for everyone, perhaps whole genome sequencing could be used in families where traditional genetic testing has proven inconclusive. Time will tell.