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Old 12-27-2011, 05:53 PM   #1
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Default Variant Frequency Calculation (non-SNP)?

Does anyone know of a program to calculate (or count) the number of nucleotides (ATCGindel) at each position of an amplicon alignment (BAM, SAM, or ACE file)?

It seems that IGV viewer outputs this data in its Coverage Track, and this is also adjustable for percentage variation. However, at this time the data is not exportable, at least, according to IGV help.

I'm performing a Directed Evolution expt on a 750 nucleotide fragment, and have run 454 titanium reads on the library. Each read has unique nucleotide variation; however, none of the variations exceeds 1% at any position. It seems that most programs are customized for dbSNP calls and call things at much higher percentages.

I am much less interested in the variant, more so the positions which have the highest variability.
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