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

[Will McLaren]

Hi Guillermo,

Thanks for this.

I'd suggest

1) make this new functionality optional. It should be enabled if the user
specifies a parameter, something like

--plugin ExAC,exac.vcf.gz,AC,AN

You can access these parameters using $self->params() in the new() method -
see the current code for how it used to get the file name

2) put in a pull request against the original plugin on our repo and we can
merge it in if it looks good.

Cheers

Will McLaren
Ensembl Variation

On 2 November 2015 at 11:32, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

> OK got it, updated version can be found on my Github mentioned on previous
> mail.
>
> The point is that "AN" was being used to get total AN, however all the
> population frequencies in ExAC are adjusted. AN_adj should be used to
> provide consistent information to the one shown in ExAC website.
> In my last commit I've added this logic, It will use AN_adj if exists and
> not zero. This shouldn't modify population allele frequencies but the total
> AN count only.
>
> Don't know if it will be useful for you too guys.
>
> Regards,
> Guillermo.
>
>
> On 02/11/15 10:43, Guillermo Marco Puche wrote:
>
> 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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