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</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=EN-GB link=blue vlink=purple><div class=WordSection1><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…<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></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'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I think what you want is:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:13.5pt'>check_frequency 1<br>freq_pop any<br>freq_freq 1<br>freq_gt_lt lt <u>(not gt”)</u><br>freq_filter include<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:13.5pt'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:13.5pt'>Best regards<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:13.5pt'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:13.5pt'>Duarte<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></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'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <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<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></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">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><o:p></o:p></p></div></body></html>