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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.<br>
<br>
<div class="moz-cite-prefix">On 02/11/15 10:43, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote cite="mid:56373050.6040606@sistemasgenomicos.com"
type="cite">
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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 moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://github.com/guillermomarco/vep_plugins/blob/master/ExAC.pm">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 moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://exac.broadinstitute.org/variant/22-46615880-T-C">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="box-sizing: border-box;
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; orphans:
auto; text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; widows: 1; word-spacing: 0px;
-webkit-text-stroke-width: 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 class="moz-cite-prefix">On 02/11/15 09:23, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote cite="mid:56371D84.5040106@sistemasgenomicos.com"
type="cite">
<meta http-equiv="content-type" content="text/html;
charset=windows-1252">
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>
<meta http-equiv="content-type" content="text/html;
charset=windows-1252">
<meta http-equiv="content-type" content="text/html;
charset=windows-1252">
<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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