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Old 12-14-2011, 04:33 PM   #5
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Location: Boston

Join Date: Feb 2008
Posts: 693

The decoy sequence resembles those unplaced and unlocalized contigs in some sense. My experience is that including those GL* contigs or not does not have a big impact on the variant accuracy. I believe the decoy sequence should not have a bigger effect in general especially after filtering. Nonetheless, decoy may be helpful when you investigate weird and rare events. I used to see two SNPs on different chromosomes are tightly linked. It turns out that one of the loci has a much better match to the Venter genome - the reference genome is missing a piece. Other strange things may happen due to an imperfect reference genome.

I guess decoy will have a bigger impact to those who work on SVs. I look forward to the results the 1000SV group will get from the phase 2 data.
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