<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Fazulur,<div class=""><br class=""></div><div class="">you are using column names in your dbNSFP argument list that are not contained in the 2.9. version. Please find the list of supported column names for version 2.9 here: <a href="https://drive.google.com/file/d/0B60wROKy6OqcdkFqMi1fNFJpZ0U/view" class="">https://drive.google.com/file/d/0B60wROKy6OqcdkFqMi1fNFJpZ0U/view</a></div><div class=""><br class=""></div><div class="">Kind regards,</div><div class="">Anja<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 21 Mar 2018, at 08:31, Rehaman <<a href="mailto:ensemblfan@gmail.com" class="">ensemblfan@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Dear Anja Thormann,</div><div class=""><br class=""></div><div class="">Thanks a lot for confirmation.</div><div class=""><br class=""></div><div class="">I used the same and ran vep with both --custom annotation feature and dbNSFP plugin, it's working now.</div><div class=""><br class=""></div><div class="">I am getting few info lines while running vep. Please find below the same.</div><div class=""><br class=""></div><div class=""><b class="">Use of uninitialized value in concatenation (.) or string at /ensembl-vep/cache/Plugins/dbNSFP.pm line 197.<br class="">Use of uninitialized value in concatenation (.) or string at /ensembl-vep/cache/Plugins/dbNSFP.pm line 197.</b></div><div class=""><b class=""><br class=""></b></div><div class="">Could you please let me know is there any issue with dbNSFP plugin.</div><div class=""><br class=""></div><div class="">Thanks In Advance</div><div class="">Fazulur Rehaman</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Mar 13, 2018 at 5:28 PM, Anja Thormann <span dir="ltr" class=""><<a href="mailto:anja@ebi.ac.uk" target="_blank" class="">anja@ebi.ac.uk</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space" class="">Dear Fazulur,<div class=""><br class=""></div><div class="">you need to use dbNSFP version 2.9.2 for GRCh37 annotations. The most recent version of dbNSFP 3.5a supports annotations for GRCh37 and GRCh38. We updated the dbNSFP plugin accordingly for our coming release/93 to work with the new file from dbNSFP. Until the new release which is planned for April I suggest that you use dbNSFP version 2.9.2.</div><div class=""><br class=""></div><div class="">Regards,</div><div class="">Anja</div><div class=""><div class="h5"><div class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On 13 Mar 2018, at 14:21, Rehaman <<a href="mailto:ensemblfan@gmail.com" target="_blank" class="">ensemblfan@gmail.com</a>> wrote:</div><br class="m_-2582148917096653062Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear Laurent,<div class=""><br class=""></div><div class="">Thanks a lot for your suggestions. I am able to use
<span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;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" class="">--custom annotation feature without errors now. And I had tried with --keep_csq option too.</span></div><div class=""><br class=""></div><div class="">Now I want to add dbNSFP annotations using dbNSFP plugin. As per documentation I installed plugins and downloaded dbNSP files.</div><div class=""><br class=""></div><div class="">Here is my command:</div><div class=""><br class=""></div><div class=""><b class="">vep -i examples/homo_sapiens_GRCh37.<wbr class="">vcf -cache --offline --dir ensembl-vep/cache --assembly GRCh37 --plugin dbNSFP,dbNSFP3.3a.txt.gz,hg19_<wbr class="">chr,genename,cds_strand,<wbr class="">refcodon,codonpos,codon_<wbr class="">degeneracy,Ancestral_allele,<wbr class="">AltaiNeandertal,Denisova,<wbr class="">Ensembl_geneid,Ensembl_<wbr class="">transcriptid,Ensembl_<wbr class="">proteinid,aapos,SIFT_score,<wbr class="">SIFT_converted_rankscore,SIFT_<wbr class="">pred,Uniprot_acc_Polyphen2</b><br class=""></div><div class=""><br class=""></div><div class="">And I am getting below error:</div><div class=""><br class=""></div><div class=""><div class=""><b class="">Use of uninitialized value $readme_file in concatenation (.) or string at /gpfs/software/genomics/vep/<wbr class="">ensembl-vep/cache/Plugins/<wbr class="">dbNSFP.pm line 157.</b></div><div class=""><b class="">Use of uninitialized value in concatenation (.) or string at /gpfs/software/genomics/vep/<wbr class="">ensembl-vep/cache/Plugins/<wbr class="">dbNSFP.pm line 197.</b></div></div><div class=""><b class=""><br class=""></b></div><div class="">I come across below post related to this plugin and it was mentioned like dbNSFP plugin is only compatible with GRCh38 build. And I am working on GRCh37. </div><div class=""><b class=""><a href="http://lists.ensembl.org/pipermail/dev/2016-February/011680.html" target="_blank" class="">http://lists.ensembl.org/<wbr class="">pipermail/dev/2016-February/<wbr class="">011680.html</a><br class=""></b></div><div class=""><br class=""></div><div class="">Could you please suggest me how to proceed further.</div><div class=""><br class=""></div><div class="">Thanks In Advance</div><div class="">Fazulur Rehaman</div><div class=""><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Mar 6, 2018 at 2:53 PM, Rehaman <span dir="ltr" class=""><<a href="mailto:ensemblfan@gmail.com" target="_blank" class="">ensemblfan@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class="">Dear Laurent,</div><div class=""><br class=""></div><div class="">Thanks for your suggestions on annotated vcf and I will try the same and let you know the status.</div><span class=""><div class=""><br class=""></div><div class="">Thanks & Regards</div><div class="">Fazulur Rehaman</div></span></div><div class="m_-2582148917096653062HOEnZb"><div class="m_-2582148917096653062h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Mar 6, 2018 at 12:09 PM, Laurent Gil <span dir="ltr" class=""><<a href="mailto:lgil@ebi.ac.uk" target="_blank" class="">lgil@ebi.ac.uk</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF" class=""><p class="">Dear Fazulur,</p><p class="">If you re-annotate a VCF file which has been already annotated by
VEP, it will add all the annotations.</p><p class="">However you have 2 options when you run VEP on your already
VEP-annotated VCF file:</p>
1 - The default behaviour si to replace the "old" annotation (CSQ)
by a "new" annotation<br class="">
2 - You can keep the "old" annotation (CSQ) in the new VCF output
and thus you will have 2 annotations per line, using the option
"--keep_csq"
<p class="">I hope it makes sense.</p><span class=""><p class="">Best regards,<br class="">
</p>
<pre class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
</span><div class=""><div class="m_-2582148917096653062m_8253614111703789905h5"><div class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958moz-cite-prefix">On 06/03/2018 07:10, Rehaman wrote:<br class="">
</div>
<blockquote type="cite" class="">
<div dir="ltr" class="">
<div class="">Dear Laurent,</div>
<div class=""><br class="">
</div>
<div class="">I have one more doubt regarding the vep annotations. I ran
vep already without gnomAD annotations before and I want to
add the same now. Can I run the same on annotated vcf file.
Does it add again all the annotations or only gnomAD
frequencies. Since we already have 1000g Allele frequencies,
sift b scores etc in our annotated vcf. Does it add again into
new annotated vcf. </div>
<div class=""><br class="">
</div>
<div class="">Could you please suggest me.</div>
<div class=""><br class="">
</div>
<div class="">Thanks & Regards</div>
<div class="">Fazulur Rehaman</div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Tue, Mar 6, 2018 at 7:28 AM, Rehaman
<span dir="ltr" class=""><<a href="mailto:ensemblfan@gmail.com" target="_blank" class="">ensemblfan@gmail.com</a>></span>
wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">
<div class="">Dear Laurent,</div>
<div class=""><br class="">
</div>
<div class="">Thanks a lot for documentation page and explanation
on custom annotation feature.</div>
<div class=""><br class="">
</div>
<div class="">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>
<span class="">
<div class=""><br class="">
</div>
<div class="">Thanks & Regards</div>
<div class="">Fazulur Rehaman</div>
</span></div>
<div class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958HOEnZb">
<div class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958h5">
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Mon, Mar 5, 2018 at 5:38
PM, Laurent Gil <span dir="ltr" class=""><<a href="mailto:lgil@ebi.ac.uk" target="_blank" class="">lgil@ebi.ac.uk</a>></span>
wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF" class=""><p class="">Dear Fazulur,</p><p class="">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 class="">
</p><p class=""><a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_options" target="_blank" class="">http://www.ensembl.org/info/do<wbr class="">cs/tools/vep/script/vep_custom<wbr class="">.html#custom_options</a><br class="">
</p><p class="">Best regards,<br class="">
</p>
<pre class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459moz-signature" cols="72">Laurent</pre>
<div class="">
<div class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958m_2482960030529164216h5">
<div class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459moz-cite-prefix">On
05/03/2018 14:27, Rehaman wrote:<br class="">
</div>
<blockquote type="cite" class="">
<div dir="ltr" class=""> <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" class="">Dear
Laurent,</span> <br class="">
<div class=""><br class="">
</div>
<div class="">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" class="">Bio:DB:HTS
perl module and issue got resolved.
Thanks a lot.</span></div>
<div class=""><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" class=""><br class="">
</span></div>
<div class=""><span style="font-size:12.8px" class="">Could
you please define what is "exact"
and "0" custom annotation feature.</span></div>
<div class=""><span style="font-size:12.8px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:12.8px" class=""> <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" class="">--custom
gnomad.exomes.r2.0.1.sites.vcf<wbr class="">.gz,gnomADg,<b class="">vcf,exact,0,</b>AF_AFR<wbr class="">,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,A<wbr class="">F_NFE,AF_OTH</span>
<br class="">
</span></div>
<div class=""><span style="font-size:12.8px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:12.8px" class="">Thanks
In Advance</span></div>
<div class=""><span style="font-size:12.8px" class="">Fazulur
Rehaman</span></div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Thu, Mar 1,
2018 at 9:58 AM, Rehaman <span dir="ltr" class=""><<a href="mailto:ensemblfan@gmail.com" target="_blank" class="">ensemblfan@gmail.com</a>></span>
wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">
<div class="">Dear Laurent,</div>
<div class=""><br class="">
</div>
<div class="">Thanks a lot for your
response.</div>
<div class=""><br class="">
</div>
<div class="">It was a typo. Actually I
have used "--" before the custom
option while running vep. </div>
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">Please suggest me if error is
not related to module.</div>
<span class="">
<div class=""><br class="">
</div>
<div class="">Thanks & Regards</div>
<div class="">Fazulur Rehaman</div>
<div class=""><br class="">
</div>
</span></div>
<div class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459HOEnZb">
<div class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459h5">
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On
Wed, Feb 28, 2018 at 12:16
PM, Laurent Gil <span dir="ltr" class=""><<a href="mailto:lgil@ebi.ac.uk" target="_blank" class="">lgil@ebi.ac.uk</a>></span>
wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF" class=""><p class="">Dear Fazulur,</p><p class="">Regarding your VEP
command it looks like
you missed to add "--"
before the "custom"
option:</p><p class=""><b class="">vep -i
[vepdir]/examples/homo_sapiens<wbr class="">_GRCh37.vcf
-cache --ASSEMBLY
GRCh37 --fork 4
--custom
gnomad.exomes.r2.0.1.sites.vcf<wbr class="">.gz,gnomADg,vcf,exact,0,AF_AFR<wbr class="">,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,A<wbr class="">F_NFE,AF_OTH</b></p><p class="">Best regards,<br class="">
</p>
<pre class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696m_-4724915924681828514moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div class="">
<div class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696h5">
<div class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696m_-4724915924681828514moz-cite-prefix">On
27/02/2018 19:04,
Rehaman wrote:<br class="">
</div>
</div>
</div>
<blockquote type="cite" class="">
<div class="">
<div class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696h5">
<div dir="ltr" class="">Dear
Ensembl team,
<div class=""><br class="">
</div>
<div class="">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 class=""><br class="">
</div>
<div class="">I tried
running vep
with example
vcf and
getting
"Segmentation
Fault" error. </div>
<div class=""><br class="">
</div>
<div class="">Command:</div>
<div class=""><br class="">
</div>
<div class=""><b class="">vep -i
[vepdir]/examples/homo_sapiens<wbr class="">_GRCh37.vcf
-cache
--ASSEMBLY
GRCh37 --fork
4 custom
gnomad.exomes.r2.0.1.sites.vcf<wbr class="">.gz,gnomADg,vcf,exact,0,AF_AFR<wbr class="">,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,A<wbr class="">F_NFE,AF_OTH</b><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Could you
please give me
suggestions on
this.</div>
<div class=""><br class="">
</div>
<div class="">Thanks
& Regards</div>
<div class="">Fazulur
Rehaman</div>
</div>
<br class="">
<fieldset class="m_-2582148917096653062m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696m_-4724915924681828514mimeAttachmentHeader"></fieldset>
<br class="">
</div>
</div>
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</blockquote>
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