<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><div><br></div><div>Thanks & Regards</div><div>Fazulur Rehaman</div><div><br></div></div><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_<wbr>sapiens_GRCh37.vcf -cache
--ASSEMBLY GRCh37 --fork 4 --custom
gnomad.exomes.r2.0.1.sites.<wbr>vcf.gz,gnomADg,vcf,exact,0,AF_<wbr>AFR,AF_AMR,AF_ASJ,AF_EAS,AF_<wbr>FIN,AF_NFE,AF_OTH</b></p>
<p>Best regards,<br>
</p>
<pre class="m_-4724915924681828514moz-signature" cols="72">Laurent
Ensembl Variation
</pre><div><div class="h5">
<div class="m_-4724915924681828514moz-cite-prefix">On 27/02/2018 19:04, Rehaman wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<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_<wbr>sapiens_GRCh37.vcf -cache
--ASSEMBLY GRCh37 --fork 4 custom
gnomad.exomes.r2.0.1.sites.<wbr>vcf.gz,gnomADg,vcf,exact,0,AF_<wbr>AFR,AF_AMR,AF_ASJ,AF_EAS,AF_<wbr>FIN,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>
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</pre>
</blockquote>
<br>
</div>
</blockquote></div><br></div>