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Old 05-20-2015, 09:27 AM   #18
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Those flags work in BBDuk as well, except for "untrim", which is unique to BBMap.

A good variant caller will take the quality into account when weighing possible variations. Quality-trimming before mapping gives the mapper less information, and thus a higher probability of ambiguously-mapped or incorrectly-mapped reads (though adapter-trimming before mapping is always good). Even if the trimmed bases are low quality - say, 50 bases at Q13 - that's still an expected 45 matches and 5 mismatches, which can greatly increase mapping confidence in a repetitive area, and thus improve the ability to call the variations from the high-quality part of the read.

On the other hand, quality-trimming before assembly is often a good idea, though the exact threshold depends on the assembler and dataset.
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