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AnamikaDarwin 07-24-2009 09:00 AM

maq 2nd and 3rd likely SNP Calls

I use the maq snp caller for snp calling on a diploid organism. The filtered maq snp report gives the most likely, 2nd likely and the 3rd likely calls.

Does anybody consider 2nd and 3rd likely calls?

When I do so, there is a certain percentage of 3-allele calls that are made and I would like to know how to "prune" this data. A naive approach would be to just trim the allele with the least counts, but it may not always work.


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