You've got a bit of misinformation in here. He's correct about the raw sequence data for a 30X whole human genome being 100GB of data. The standard practice is

You've got a bit of misinformation in here. He's correct about the raw sequence data for a 30X whole human genome being 100GB of data. The standard practice is to align the sample to the reference, but we store alignments in the BAM file, not variations. Some of the mismatches in the alignments are due to noise in the sequencer. We run the BAM through a variant caller which outputs a VCF which contains the variants. You do not typically genotype at only known SNP sites when generating a VCF file (although you may restrict by a region). If you were only interested in certain SNP sites you would be better off running a microarray.