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Old 05-31-2012, 11:14 AM   #2
Location: CA, USA

Join Date: May 2012
Posts: 72

Most base callers either call "n" at SNP location or pick one or the other (combination of sharpest peak and highest peak as scaled to average intensity for that base). Very few use IUPAC ambiguity codes to convey the potential difference. Quality for those locations, assuming an unbiased amplification level should be approximately 1/2 of the surrounding bases (I believe it's linearly scaled at least). So, if scripts don't already exist, you should be able to compare quality from one base to the neighboring two bases and see if the qual is significantly lower. Then you look at the trace itself (if available) to see if this is a potential SNP.

It's more difficult if it's a "chimera" or extended polymorphism or if there's a "frameshift."

I'd be interested to know if there are any chimera/SNP deconvolver programs or scripts out there for use that I can supply the reference sequence and it can let me know the alternate read. I was staring at at two overlapping reads that were significantly out-of-phase with each other yesterday and made about 50 base calls manually over an hour or two. Hardly the model of efficiency
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