<div dir="ltr"><div>Dear Laurent,</div><div><br></div><div>Thanks a lot for quick response and I will use the same till new release.</div><div><br></div><div>Thanks & Regards</div><div>Fazulur Rehaman</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 13, 2018 at 5:28 PM, Anja Thormann <span dir="ltr"><<a href="mailto:anja@ebi.ac.uk" target="_blank">anja@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 style="word-wrap:break-word;line-break:after-white-space">Dear Fazulur,<div><br></div><div>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><br></div><div>Regards,</div><div>Anja</div><div><div class="h5"><div><div><br><blockquote type="cite"><div>On 13 Mar 2018, at 14:21, Rehaman <<a href="mailto:ensemblfan@gmail.com" target="_blank">ensemblfan@gmail.com</a>> wrote:</div><br class="m_8049561984213244222Apple-interchange-newline"><div><div dir="ltr">Dear Laurent,<div><br></div><div>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">--custom annotation feature without errors now. And I had tried with --keep_csq option too.</span></div><div><br></div><div>Now I want to add dbNSFP annotations using dbNSFP plugin. As per documentation I installed plugins and downloaded dbNSP files.</div><div><br></div><div>Here is my command:</div><div><br></div><div><b>vep -i examples/homo_sapiens_GRCh37.<wbr>vcf -cache --offline --dir ensembl-vep/cache --assembly GRCh37 --plugin dbNSFP,dbNSFP3.3a.txt.gz,hg19_<wbr>chr,genename,cds_strand,<wbr>refcodon,codonpos,codon_<wbr>degeneracy,Ancestral_allele,<wbr>AltaiNeandertal,Denisova,<wbr>Ensembl_geneid,Ensembl_<wbr>transcriptid,Ensembl_<wbr>proteinid,aapos,SIFT_score,<wbr>SIFT_converted_rankscore,SIFT_<wbr>pred,Uniprot_acc_Polyphen2</b><br></div><div><br></div><div>And I am getting below error:</div><div><br></div><div><div><b>Use of uninitialized value $readme_file in concatenation (.) or string at /gpfs/software/genomics/vep/<wbr>ensembl-vep/cache/Plugins/<wbr>dbNSFP.pm line 157.</b></div><div><b>Use of uninitialized value in concatenation (.) or string at /gpfs/software/genomics/vep/<wbr>ensembl-vep/cache/Plugins/<wbr>dbNSFP.pm line 197.</b></div></div><div><b><br></b></div><div>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><b><a href="http://lists.ensembl.org/pipermail/dev/2016-February/011680.html" target="_blank">http://lists.ensembl.org/<wbr>pipermail/dev/2016-February/<wbr>011680.html</a><br></b></div><div><br></div><div>Could you please suggest me how to proceed further.</div><div><br></div><div>Thanks In Advance</div><div>Fazulur Rehaman</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 6, 2018 at 2:53 PM, 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 for your suggestions on annotated vcf and I will try the same and let you know the status.</div><span><div><br></div><div>Thanks & Regards</div><div>Fazulur Rehaman</div></span></div><div class="m_8049561984213244222HOEnZb"><div class="m_8049561984213244222h5"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 6, 2018 at 12:09 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>If you re-annotate a VCF file which has been already annotated by
VEP, it will add all the annotations.</p><p>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>
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>I hope it makes sense.</p><span><p>Best regards,<br>
</p>
<pre class="m_8049561984213244222m_8253614111703789905m_7859209184321000958moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
</span><div><div class="m_8049561984213244222m_8253614111703789905h5"><div class="m_8049561984213244222m_8253614111703789905m_7859209184321000958moz-cite-prefix">On 06/03/2018 07:10, Rehaman wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Dear Laurent,</div>
<div><br>
</div>
<div>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><br>
</div>
<div>Could you please suggest me.</div>
<div><br>
</div>
<div>Thanks & Regards</div>
<div>Fazulur Rehaman</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Mar 6, 2018 at 7:28 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 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>
<span>
<div><br>
</div>
<div>Thanks & Regards</div>
<div>Fazulur Rehaman</div>
</span></div>
<div class="m_8049561984213244222m_8253614111703789905m_7859209184321000958HOEnZb">
<div class="m_8049561984213244222m_8253614111703789905m_7859209184321000958h5">
<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">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>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">http://www.ensembl.org/info/do<wbr>cs/tools/vep/script/vep_custom<wbr>.html#custom_options</a><br>
</p><p>Best regards,<br>
</p>
<pre class="m_8049561984213244222m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459moz-signature" cols="72">Laurent</pre>
<div>
<div class="m_8049561984213244222m_8253614111703789905m_7859209184321000958m_2482960030529164216h5">
<div class="m_8049561984213244222m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-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,A<wbr>F_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>
<div><br>
</div>
<div>Thanks & Regards</div>
<div>Fazulur Rehaman</div>
<div><br>
</div>
</span></div>
<div class="m_8049561984213244222m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459HOEnZb">
<div class="m_8049561984213244222m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-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">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,A<wbr>F_NFE,AF_OTH</b></p><p>Best regards,<br>
</p>
<pre class="m_8049561984213244222m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696m_-4724915924681828514moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div>
<div class="m_8049561984213244222m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696h5">
<div class="m_8049561984213244222m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696m_-4724915924681828514moz-cite-prefix">On
27/02/2018 19:04,
Rehaman wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="m_8049561984213244222m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-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>
<br>
<fieldset class="m_8049561984213244222m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696m_-4724915924681828514mimeAttachmentHeader"></fieldset>
<br>
</div>
</div>
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