They aren't actually sequencing the whole DNA, they are just searching it for SNPs (single-nucleotide polymorphisms) that have previously been discovered in the human genome. For example if they know there is sequence such as AAAC[CG]CTTA in the genome ([CG] being either C or G) they will check which of AAACCCTTA and AAACGCTTA they can find.
So as much as i hate to give such a boring answer, this would probably just result in them not being able to use the sample.
So as much as i hate to give such a boring answer, this would probably just result in them not being able to use the sample.