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Should Indels Get Special Treatment?

Oct 04, 2008

Mike the Mad Biologist reaches out for help analyzing indel data. He's using Illumina to generate lists of SNPs for many different bacterial strains, but has found that anywhere from ten to forty percent of the SNPs are indels. His question for fellow researchers is, should he use a statistical analysis program that treats the indels as single characters or not? "I would note that as it gets really cheap to scan entire microbial genomes for SNPs, this will be a problem we have to grapple with," he says.

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