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

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Mon Nov 2 08:23:32 GMT 2015


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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