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<p>Dear Fazulur,</p>
<p>You can see the explanations about the custom annotation options
(i.e. "exact" => "Annotation type" and "0" => "Force report
coordinates" flag) in the VEP documentation page: <br>
</p>
<p><a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_options">http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_options</a><br>
</p>
<p>Best regards,<br>
</p>
<pre class="moz-signature" cols="72">Laurent</pre>
<div class="moz-cite-prefix">On 05/03/2018 14:27, Rehaman wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAOnJw46imYc7vncRFgJXa3+sjM76RAbxywtgG4Vgho1tE8UtkA@mail.gmail.com">
<div dir="ltr">
<span
style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Dear
Laurent,</span>
<br>
<div><br>
</div>
<div>I have installed
<span
style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Bio:DB:HTS
perl module and issue got resolved. Thanks a lot.</span></div>
<div><span
style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br>
</span></div>
<div><span style="font-size:12.8px">Could you please define what
is "exact" and "0" custom annotation feature.</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">
<span
style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">--custom
gnomad.exomes.r2.0.1.sites.<wbr>vcf.gz,gnomADg,<b>vcf,exact,0,</b>AF_<wbr>AFR,AF_AMR,AF_ASJ,AF_EAS,AF_<wbr>FIN,AF_NFE,AF_OTH</span>
<br>
</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">Thanks In Advance</span></div>
<div><span style="font-size:12.8px">Fazulur Rehaman</span></div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Mar 1, 2018 at 9:58 AM, Rehaman
<span dir="ltr"><<a href="mailto:ensemblfan@gmail.com"
target="_blank" moz-do-not-send="true">ensemblfan@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Dear Laurent,</div>
<div><br>
</div>
<div>Thanks a lot for your response.</div>
<div><br>
</div>
<div>It was a typo. Actually I have used "--" before the
custom option while running vep. </div>
<div><br>
</div>
<div>May be Segmentation fault error is due to Bio:DB:HTS
perl module. I will run again after installing the same
and let you know the status.</div>
<div><br>
</div>
<div>Please suggest me if error is not related to module.</div>
<span class="">
<div><br>
</div>
<div>Thanks & Regards</div>
<div>Fazulur Rehaman</div>
<div><br>
</div>
</span></div>
<div class="HOEnZb">
<div class="h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Feb 28, 2018 at 12:16
PM, Laurent Gil <span dir="ltr"><<a
href="mailto:lgil@ebi.ac.uk" target="_blank"
moz-do-not-send="true">lgil@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<p>Dear Fazulur,</p>
<p>Regarding your VEP command it looks like you
missed to add "--" before the "custom" option:</p>
<p><b>vep -i [vepdir]/examples/homo_sapiens<wbr>_GRCh37.vcf
-cache --ASSEMBLY GRCh37 --fork 4 --custom
gnomad.exomes.r2.0.1.sites.vcf<wbr>.gz,gnomADg,vcf,exact,0,AF_AFR<wbr>,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,<wbr>AF_NFE,AF_OTH</b></p>
<p>Best regards,<br>
</p>
<pre class="m_5520331521785988696m_-4724915924681828514moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div>
<div class="m_5520331521785988696h5">
<div
class="m_5520331521785988696m_-4724915924681828514moz-cite-prefix">On
27/02/2018 19:04, Rehaman wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="m_5520331521785988696h5">
<div dir="ltr">Dear Ensembl team,
<div><br>
</div>
<div>I am running VEP for GRCh37
assembly and as you mentioned some of
alleles may not get Allele frequencies
and so I want to test custom
annotation optio</div>
<div><br>
</div>
<div>I tried running vep with example
vcf and getting "Segmentation Fault"
error. </div>
<div><br>
</div>
<div>Command:</div>
<div><br>
</div>
<div><b>vep -i
[vepdir]/examples/homo_sapiens<wbr>_GRCh37.vcf
-cache --ASSEMBLY GRCh37 --fork 4
custom
gnomad.exomes.r2.0.1.sites.vcf<wbr>.gz,gnomADg,vcf,exact,0,AF_AFR<wbr>,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,<wbr>AF_NFE,AF_OTH</b><br>
</div>
<div><br>
</div>
<div>Could you please give me
suggestions on this.</div>
<div><br>
</div>
<div>Thanks & Regards</div>
<div>Fazulur Rehaman</div>
</div>
<br>
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</pre>
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