<div dir="ltr">Correct, but if you just want to display the frequencies without filtering, just use --gmaf and --maf_1kg - to do otherwise just wastes processing time!<div><br></div><div style>Will</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On 29 May 2013 09:14, Duarte Molha <span dir="ltr"><<a href="mailto:Duarte.Molha@ogt.com" target="_blank">Duarte.Molha@ogt.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="white" lang="EN-GB" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Correct me if I am wrong Will… but I believe that the arguments Guillermo is using are not adequate…<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Guillermo…If I understand correctly with your arguments you are requesting the script to check for frequencies and include all with a frequency above 1… Obviously there is no variant with a frequency above 1 </span><span style="font-size:11.0pt;font-family:Wingdings;color:#1f497d">J</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I think what you want is:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:13.5pt"></span></p><div class="im">
check_frequency 1<br>freq_pop any<br>freq_freq 1<br></div>freq_gt_lt lt <u>(not gt”)</u><br>freq_filter include<u></u><u></u><p></p><p class="MsoNormal"><span style="font-size:13.5pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:13.5pt">Best regards<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:13.5pt"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:13.5pt">Duarte<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<div><div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"><p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>] <b>On Behalf Of </b>Guillermo Marco Puche<br>
<b>Sent:</b> 28 May 2013 16:33<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> [ensembl-dev] VEP populations frequency on output<u></u><u></u></span></p></div></div><div><div class="h5"><p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:13.5pt">Hello !<br><br>Currently I'm using <b>gmaf</b> and <b>maf_1kg</b> options.<br><br>On my output AFR_MAF, AMR_MAF, ASN_MAF, EUR_MAF are always being reported empty "-". Just GMAF is being reported non empty.<br>
I want population frequency to be reported from 0 to maximum. I mean report all values I can.<br><br>I've tried adding the following options:<br><br>check_frequency 1<br>freq_pop any<br>freq_freq 1<br>
freq_gt_lt gt<br>freq_filter include<br><br><br>This does include more lines to VEP output but all the columns still empty.<br><br>Here's a variation example where other population should be reported: <br>
<br><a href="http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=1:11905298-11906308;v=rs144578530;vdb=variation;vf=35767060" target="_blank">http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=1:11905298-11906308;v=rs144578530;vdb=variation;vf=35767060</a><br>
<br>I don't know if this is a bug or I'm misunderstanding how it works. As I said I want all freqs to be reported without any minium or filter.<br><br>Thanks !<br><br>Best regards,<br>Guillermo</span><u></u><u></u></p>
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