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</o:shapelayout></xml><![endif]--></head><body 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'>Any views on this?<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'>Thanks<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>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><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Duarte Molha<br><b>Sent:</b> 22 May 2013 13:17<br><b>To:</b> Ensembl<br><b>Subject:</b> Re: [ensembl-dev] Feature request (Allele variant Frequency)<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Also, in addition to this, I could probably use the frequency flags to they all information i need and then parse it later on...<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>like <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><div><p class=MsoNormal>check_frequency 1<o:p></o:p></p></div><div><p class=MsoNormal>freq_filter include<o:p></o:p></p></div><div><p class=MsoNormal>freq_freq 1<o:p></o:p></p></div><div><p class=MsoNormal>freq_gt_lt lt<o:p></o:p></p></div><div><p class=MsoNormal>freq_pop any<o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>However, this is cumbersome and also removes all other variants from the output that have no frequency information.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thanks<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Duarte<o:p></o:p></p></div></div><div><p class=MsoNormal><br clear=all><o:p></o:p></p><div><p class=MsoNormal><span style='color:#999999;background:white'>=========================<br> Duarte Miguel Paulo Molha </span><o:p></o:p></p><div><p class=MsoNormal><span style='color:#999999;background:white'> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</span><o:p></o:p></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On Wed, May 22, 2013 at 11:57 AM, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal>I am not sure if you have already addressed this question Will<o:p></o:p></p></div><div><p class=MsoNormal>But I would like to request that a additional option be included for annotation output.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Currently the GMAF of a given known variation is output with the --GMAF flag<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>However, this does not give us the frequency of the seen allele on out sample.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>say their is a variation <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>like so<o:p></o:p></p></div><div><p class=MsoNormal>ref_allele alt_alleles<o:p></o:p></p></div><div><p class=MsoNormal>C A,T<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>And our sample has a genotype 1,2<o:p></o:p></p></div><div><p class=MsoNormal>and the GMAF gives us GMAF=A:0.2399<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>In this case it is not possible to determine the allelic frequency of the other allele present in the sample.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Ideally there should be a flag like --allele_freq that would five you the allele for the allele present in the sample.<o:p></o:p></p></div><div><p class=MsoNormal>You must already be calculating this because you have fields for filtering variation based on their frequency in any given population ,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Best regards<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Duarte<o:p></o:p></p></div><p class=MsoNormal><br clear=all><o:p></o:p></p><div><p class=MsoNormal><span style='color:#999999'>=========================<br> Duarte Miguel Paulo Molha </span><o:p></o:p></p><div><p class=MsoNormal><span style='color:#999999'> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</span><o:p></o:p></p></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>