Hi Josh,
the program does what it says in the documentation, it is not a typo.
Best wishes,
Petr
On Thu, 2015-06-11 at 14:17 -0400, Joshua Bradley wrote:
> Hello, I have been reading this documentation that details the math
> behind how bcftools calls a genotype and I am not sure whether or not
> equation (1) is wrong. The document says the following equation is
> used to calculate allele frequencies
>
>
> f_x = sum_k( Q_k^x) / sum_{k,y}( Q_k^y )
>
>
> As stated in the document, Q is defined as the (base) quality and D_x
> is defined as the number of times a base x has been seen. With that
> being said, I would think the allele frequency would be calculated as
>
>
> f_x = D_x / sum_y( D_y )
>
>
>
> Hopefully my notation conveys the idea I'm trying make. Does
> samtools/bcftools calculate allele frequency using the base quality
> formula like the document says or does it assume the base calls are
> 100% correct and calculate the allele frequency using the above
> formula I made? If the latter is true, then I think there is a typo in
> the documentation.
>
> Josh Bradley
>
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