I am trying to estimate the frequency of SNP occurence in my library as reported by the maq aligner. The quick and dirty way of doing this, I believe, is to calculate the number of bases of the reference genome that are covered by at least 3 uniquely mapped reads. That should match the cutoff specified in SNPFilter command of maq. Does anyone know if this information is available somewhere in the maq output files?
Also, please let me know if you think my logic for estimating the frequency is blatantly wrong. I understand that its not perfect but this is just my first hack at it.
Also, please let me know if you think my logic for estimating the frequency is blatantly wrong. I understand that its not perfect but this is just my first hack at it.
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