I'm interested to hear what kind of filtering people are using for homopolymer expansion variants, and what expectations are of the accuracy of those variant calls. When you see a variant with alleles like GAAAAAA/GAAAAAAA in Illumina output, do you assume that it is a sequencing artifact?
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The Illumina sequencing process is much less prone to homopolymer sequencing error compared to 454 and IonTorrent/IonProton, so you can be fairly sure about homopolymer runs of high quality.
That doesn't mean it won't happen. Due to the stochastic nature of the sequencing process (or "phasing" issues), it is possible that there is a a failed (or additional) incorporation, which may not be treated as an error until the next non-homopolymer base. I don't think there are programs available that take this into account, but I would be hesitant to accept as real a homopolymer run that was followed by bases with very low quality scores.
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