A Whole Genome Mess

A whole-genome sequencing paper coming out in Genome Research used ABI's SOLiD platform to sequence the same person that the Illumina paper did, as Dan Koboldt points out. The SOLiD paper authors did not compare the sequences citing, in the comments to Koboldt's blog, the Illumina paper's lack of genotype information. And so in a guest post at Daniel MacArthur's blog, Luke Jostins embarks on that himself. Jostins says that the SOLiD paper is "the most in-depth study of variation within a single human genome" and it reports a number of indels, inversions, and hundreds of CNVs. Compared to Illumina, he says SOLiD "matched their SNP calling for quality, beat them in range (if not quantity) of indel sizes, and do a load of other fancy tricks, all for less than half the coverage." However, Jostins adds that in the paper, SOLiD used a few "tricks." "But to do this, they had to fudge a few things: get the coverage down by cutting out lots of reads, obfuscate the low quality of heterozygous calls, and give an overenthusiastic estimate of how cheap their technology is," he writes.