[Vcftools-help] Probleme with VCFtool allel frequency

[Kazmierczak S. <ste...@gm...>]

Hello I am having problem using VCFTool to compute allele frequency
the program doesn't take into account reference individual in the
denominator

for example out of my 17 samples one has 1/0 variant letter G replace by A
then the output of VCFTool report nchr 2 freq G0.5 A0.5

the problem is that the frequency for the variant A is 1/34 ~= 0.029
somehow I could calculate the frequency that I want using nchr * freq /
(sample * all_number)
but I then have a problem for missing value.

Indeed on another variant line I have 3 samples with 1/. variant letter A
replace G
and the output of VCFTool report n_ch 3 freq A:0 G:1 so in this case to
calculate frequency I would need to subtract from the denominator the
number of errors or "." for the line.

Is there a way to get number of errors/missing calls?