Thread: BFAST published
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Old 11-20-2009, 11:42 AM   #12
Nils Homer
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Location: Boston, MA, USA

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Originally Posted by Michael.James.Clark View Post
Congratulations, Nils!

It makes sense to me that they would have higher false positive rates at zero errors because they identify significantly more true positives as well (as 3A is basically gauging true positives and 3B is gauging false positives). My guess is that they are aligning questionable reads that the other aligners are not aligning at all in order to have a higher yield of true positives. I would pose the question of whether one can get BWA and Bowtie to generate fewer false positives, and how that would thereby affect their true positive yield at zero errors. (I have not used them personally, so it's an open question.) Then again, I think it's rather a moot point. The figure is basically demonstrating to me that all of these aligners do quite well at zero-two nucleotide errors.

What I find more striking in that particular figure is how they perform with high error reads, but even more strikingly, reads containing deletions (even deletions of a relatively large size). This is important to me because a lot of studies, particularly whole genome, are searching for novel variants and deletions with relatively low coverage.

Anyway, we have had great success using BFAST on whole genome data from the SOLiD platform, so I am really happy to see it finally published and encourage others to try it.
At zero errors and no variants, Heng Li is saying that there should be zero false positives, although there could be false-negatives.
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