<div dir="ltr">Hi Guillermo,<div><br></div><div>Thanks for this.</div><div><br></div><div>I'd suggest</div><div><br></div><div>1) make this new functionality optional. It should be enabled if the user specifies a parameter, something like</div><div><br></div><div>--plugin ExAC,exac.vcf.gz,AC,AN</div><div><br></div><div>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</div><div><br></div><div>2) put in a pull request against the original plugin on our repo and we can merge it in if it looks good.</div><div><br></div><div>Cheers</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 2 November 2015 at 11:32, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066">
OK got it, updated version can be found on my Github mentioned on
previous mail.<br>
<br>
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.<br>
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.<br>
<br>
Don't know if it will be useful for you too guys.<br>
<br>
Regards,<br>
Guillermo.<div><div class="h5"><br>
<br>
<div>On 02/11/15 10:43, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote type="cite">
Hello Will,<br>
<br>
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: <a href="https://github.com/guillermomarco/vep_plugins/blob/master/ExAC.pm" target="_blank">https://github.com/guillermomarco/vep_plugins/blob/master/ExAC.pm</a><br>
<br>
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 (<a href="http://exac.broadinstitute.org/variant/22-46615880-T-C" target="_blank">http://exac.broadinstitute.org/variant/22-46615880-T-C</a>):<br>
<br>
22 46615880 rs1800234 T C .
. AA=T<br>
<br>
All the counts per population and frequencies are identical to
those in ExAC website, however for the totals I'm getting:<br>
<ul>
<li>Allele count: 1163 (OK)</li>
<li>Allele number: 121412 (this differs from ExAC website that
shows<b> 120986</b><b style="font-weight:bold;color:rgb(51,51,51);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:14px;font-style:normal;font-variant:normal;letter-spacing:normal;line-height:11.4286px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255)"> and its the correct sum total of all the pops)</b></li>
</ul>
<p>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.<br>
</p>
<p>Regards,<br>
Guillermo.<br>
</p>
<div>On 02/11/15 09:23, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote type="cite">
Hello Will,<br>
<br>
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:<br>
<br>
<pre style="background-color:#2b2b2b;color:#a9b7c6;font-family:'Source Code Pro';font-size:13.5pt"> <span style="color:#cc7832">foreach my </span>$a(@vcf_alleles) {
<span style="color:#cc7832">my </span>$ac = <span style="color:#ab51ba">shift </span>@ac;
$total_ac += $ac;
$data->{$a}->{<span style="color:#6a8759">'ExAC_'</span>.$afh.<span style="color:#6a8759">'_AC'</span>} = $ac;
$data->{$a}->{<span style="color:#6a8759">'ExAC_'</span>.$afh.<span style="color:#6a8759">'_AN'</span>} = $an;
$data->{$a}->{<span style="color:#6a8759">'ExAC_'</span>.$afh} = sprintf(<span style="color:#6a8759">"%.3g"</span>, $ac / $an);
}
<span style="color:#808080;font-style:italic"># use total to get ref allele freq
</span><span style="color:#808080;font-style:italic"> </span>$data->{$ref_allele}->{<span style="color:#6a8759">'ExAC_'</span>.$afh.<span style="color:#6a8759">'_AC'</span>} = $total_ac;
$data->{$ref_allele}->{<span style="color:#6a8759">'ExAC_'</span>.$afh.<span style="color:#6a8759">'_AN'</span>} = $an;
$data->{$ref_allele}->{<span style="color:#6a8759">'ExAC_'</span>.$afh} = sprintf(<span style="color:#6a8759">"%.3g"</span>, <span style="color:#6897bb">1 </span>- ($total_ac / $an));
}</pre>
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.<br>
<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
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