[ensembl-dev] Plugin: ExAC print AC/AN for each population

[Guillermo Marco Puche]

Hello Will,

I've come up with a modified version of your ExAC plugin that writes 
AC/AN counts per pop to the output you can check the code here: 
https://github.com/guillermomarco/vep_plugins/blob/master/ExAC.pm

However debugging this for the new columns I've found a bug. I'm testing 
the script with the following mutation that has ExAC information 
(http://exac.broadinstitute.org/variant/22-46615880-T-C):

22      46615880        rs1800234       T       C       . .       AA=T

All the counts per population and frequencies are identical to those in 
ExAC website, however for the totals I'm getting:

  * Allele count: 1163 (OK)
  * Allele number: 121412 (this differs from ExAC website that
    shows*120986**and its the correct sum total of all the pops)*

Maybe there's something else being added up, but I can't find where's 
the problem since all individual allele pop counts are OK. Gonna check 
ExAC VCF for this position to see if I can any clue.

Regards,
Guillermo.

On 02/11/15 09:23, Guillermo Marco Puche wrote:
> Hello Will,
>
> I'm interested to print AC and AN count for each population in ExAC 
> VEP plugin output. I've modified the following lines to store the data:
>
>    foreach my $a(@vcf_alleles) {
>      my $ac =shift @ac;
>      $total_ac += $ac;
>      $data->{$a}->{'ExAC_'.$afh.'_AC'} = $ac;
>      $data->{$a}->{'ExAC_'.$afh.'_AN'} = $an;
>      $data->{$a}->{'ExAC_'.$afh} = sprintf("%.3g", $ac / $an);
>    }
>
>    # use total to get ref allele freq $data->{$ref_allele}->{'ExAC_'.$afh.'_AC'} = $total_ac;
>    $data->{$ref_allele}->{'ExAC_'.$afh.'_AN'} = $an;
>    $data->{$ref_allele}->{'ExAC_'.$afh} = sprintf("%.3g",1 - ($total_ac / $an));
> }
> However I'm getting a bit messy when it comes to header function. It 
> loops over ExAC header, but I don't know how to modify 
> get_header_info() to output the desired columns.
>
>
> Regards,
> Guillermo.
>
>
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