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Seems like better representation could save a few orders of magnitude in data size. Humans only differ at about 1/1000 nucleotides so storing just differences rather than all genomic positions should greatly alleviate the issue. In theory you would just have to store less than a megabyte of nucleotides per personal genome. Probably have to get rid of one-off sequencing errors and quality scores at some point as scaling up to planet wide genomic sequencing.

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Better representations are already used for downstream data analysis and continue to be improved; see e.g. http://arxiv.org/abs/1506.08452 .

However, algorithms for producing variant calls from raw sequencer output are also improving over time, and the way to get the most benefit from them is to save the old raw data so newer algorithms can be applied to them. That's where the storage challenges come into play.

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