[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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20151102/95252bd6/attachment.html>
More information about the Dev
mailing list