<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">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">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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<br>
</div></div><pre>______________________________<wbr>_________________
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</pre>
</blockquote>
<br>
</div>
</blockquote></div><br></div>
</div></div></blockquote></div><br></div>