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<p>Dear Fazulur,</p>
<p>I don't see any problem to use the "--everything" and "--custom"
options together.</p>
<p>Best regards,<br>
</p>
<pre class="moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div class="moz-cite-prefix">On 06/03/2018 04:28, Rehaman wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAOnJw45_X_S6sOp=c+GZJL+aSrG01MRW84gktbx0imw0Fpzwfw@mail.gmail.com">
<div dir="ltr">
<div>Dear Laurent,</div>
<div><br>
</div>
<div>Thanks a lot for documentation page and explanation on
custom annotation feature.</div>
<div><br>
</div>
<div>As "--everything" option contains other annotations (--sift
b, --polyphen, --hgcs etc), can we use "--everything" and
"--custom" (for missing gnomAD allele frequencies) options
together with vep. Please confirm?</div>
<div><br>
</div>
<div>Thanks & Regards</div>
<div>Fazulur Rehaman</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Mar 5, 2018 at 5:38 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 text="#000000" bgcolor="#FFFFFF">
<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
href="http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_options"
target="_blank" moz-do-not-send="true">http://www.ensembl.org/info/<wbr>docs/tools/vep/script/vep_<wbr>custom.html#custom_options</a><br>
</p>
<p>Best regards,<br>
</p>
<pre class="m_-6995096064473700459moz-signature" cols="72">Laurent</pre>
<div>
<div class="h5">
<div class="m_-6995096064473700459moz-cite-prefix">On
05/03/2018 14:27, Rehaman wrote:<br>
</div>
<blockquote type="cite">
<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.vcf<wbr>.gz,gnomADg,<b>vcf,exact,0,</b>AF_AFR<wbr>,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,<wbr>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>
<div><br>
</div>
<div>Thanks & Regards</div>
<div>Fazulur Rehaman</div>
<div><br>
</div>
</span></div>
<div class="m_-6995096064473700459HOEnZb">
<div class="m_-6995096064473700459h5">
<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 text="#000000"
bgcolor="#FFFFFF">
<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,A<wbr>F_NFE,AF_OTH</b></p>
<p>Best regards,<br>
</p>
<pre class="m_-6995096064473700459m_5520331521785988696m_-4724915924681828514moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div>
<div
class="m_-6995096064473700459m_5520331521785988696h5">
<div
class="m_-6995096064473700459m_5520331521785988696m_-4724915924681828514moz-cite-prefix">On
27/02/2018 19:04, Rehaman
wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div
class="m_-6995096064473700459m_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,A<wbr>F_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>
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