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<div style="font-family: Consolas;">Thanks Will – much appreciated! </div>
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<div style="font-family: Consolas;">Regards</div>
<div style="font-family: Consolas;">alex </div>
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<div style="font-family: Consolas;">Message: 1</div>
<div style="font-family: Consolas;">Date: Mon, 26 Oct 2015 13:34:50 +0000</div>
<div style="font-family: Consolas;">From: Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>></div>
<div style="font-family: Consolas;">Subject: Re: [ensembl-dev] VEP filter for 100 Genome Frequencies at</div>
<div style="font-family: Consolas;"><span class="Apple-tab-span" style="white-space: pre;"></span>single base indwells</div>
<div style="font-family: Consolas;">To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>></div>
<div style="font-family: Consolas;">Message-ID:</div>
<div style="font-family: Consolas;"><span class="Apple-tab-span" style="white-space: pre;"></span><<a href="mailto:CAMVEDX1x2AWiWSo9GZwXNoYx7wfS1CVP5C93014R-Fa6swk_VQ@mail.gmail.com">CAMVEDX1x2AWiWSo9GZwXNoYx7wfS1CVP5C93014R-Fa6swk_VQ@mail.gmail.com</a>></div>
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<div style="font-family: Consolas;">Hi Alex,</div>
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<div style="font-family: Consolas;">I've committed a fix for this issue to the ensembl-tools repo (on the</div>
<div style="font-family: Consolas;">release/82 branch); you'll need to re-download it to get the fix, or use</div>
<div style="font-family: Consolas;">"git pull" if you happened to use git to fetch the repo in the first place.</div>
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<div style="font-family: Consolas;">Regards</div>
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<div style="font-family: Consolas;">Will</div>
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<div style="font-family: Consolas;">On 26 October 2015 at 08:51, Alex Beesley <<a href="mailto:Alex.Beesley@telethonkids.org.au">Alex.Beesley@telethonkids.org.au</a>></div>
<div style="font-family: Consolas;">wrote:</div>
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<blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="font-family: Consolas; border-left-color: rgb(181, 196, 223); border-left-width: 5px; border-left-style: solid; padding: 0px 0px 0px 5px; margin: 0px 0px 0px 5px;">
<div>Hi team ? I have been using the VEP filter script to filter variants based</div>
<div>on 1000 Genome frequencies (--filter "GMAF not > 0.01?), but this doesn?t</div>
<div>seem to recognise frequencies for single base indels.</div>
<div>For example, the following is a high frequency indel for which the base is</div>
<div>not indicated because it is a deletion. But one would still want to filter</div>
<div>it out.</div>
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<div>rs142545439</div>
<div>GMAF</div>
<div> -:0.3706</div>
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<div>Unfortunately the VEP filter does not seem to recognise the format of</div>
<div>these frequencies and refuses to cooperate with any of the operators (e.g.</div>
<div> < or >). The same applies to all the other 1000Genome population</div>
<div>frequencies. Help!</div>
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<div>Thanks in advance</div>
<div>Alex</div>
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