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Old 06-02-2012, 12:13 PM   #3
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Location: Boston

Join Date: Feb 2008
Posts: 693

Mapping based approach may be confused by long indels or large-scale changes, which leads to false SNPs. This is not that infrequent for human SNP discovery. Assembly can do better in such cases as it more effectively takes advantage of between-read information.

On the other hand, although I believe for small genomes, assembly based approach is advantageous in theory, many existing assemblers and contig aligners are not fine tuned for assembly based SNP discovery. On Illumina data, for which the tool chain is relatively complete and mature, the overall accuracy of mapping based calls is likely to be better unless you are very careful about the assembly.

Anyway, which is better highly depends on how you did the analysis and the divergence from your reference. We cannot just tell from the numbers. I recommend you look at calls unique to one set in IGV/tview and get a sense by yourself. This is the cheapest yet very effective way to answer your own question.
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