Any user friendly way to find rare mutations in whole genome raw?
You need to run a SNP finding pipeline, filter for SNPs in those genes and then run a SNP annotation pipeline. (You could annotate before you filter but it will take longer).

SNP finding usually has three steps, 1) read alignment to reference, 2) SNP calling and 3) SNP filtering (by quality).

You then bring in gene annotation data to filter SNPs to just those genes.

You then run SNP annotation using tools like VEP, SIFT, PolyPhen, etc.

People use tools like GATK to do this.

Hopefully that's enough information to get you started.