[ensembl-dev] Plugin: ExAC print AC/AN for each population
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Mon Nov 2 09:43:44 GMT 2015
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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