Thread: BFAST published
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Old 11-11-2009, 08:55 AM   #4
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Join Date: Feb 2008
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I did not read into details, but something is a little bit odd in Figure 3. How can bowtie and bwa produce wrong alignments even if the read can be perfectly mapped? For perfectly aligned reads, both of them should always give correct results. Also note that 6% error is really a lot. If an aligner was that bad, it would not survive these days. Nonetheless, I agree that the performance of bwa degrades with higher error/mutation rate.

In SNP calling given short reads, alignment global to reads has some advantage. Suppose the 3rd base in a read is a true mutation. Local alignment will clip the read and as a result you see more reads having the reference allele than having the non-reference allele, which leads to strong reference bias. To alleviate this bias, we need to postprocess local alignments.
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