<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.vcf -cache --offline --dir ensembl-vep/cache --assembly GRCh37 --plugin dbNSFP,dbNSFP3.3a.txt.gz,hg19_chr,genename,cds_strand,refcodon,codonpos,codon_degeneracy,Ancestral_allele,AltaiNeandertal,Denisova,Ensembl_geneid,Ensembl_transcriptid,Ensembl_proteinid,aapos,SIFT_score,SIFT_converted_rankscore,SIFT_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/ensembl-vep/cache/Plugins/dbNSFP.pm line 157.</b></div><div><b>Use of uninitialized value in concatenation (.) or string at /gpfs/software/genomics/vep/ensembl-vep/cache/Plugins/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">http://lists.ensembl.org/pipermail/dev/2016-February/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 class=""><div><br></div><div>Thanks & Regards</div><div>Fazulur Rehaman</div></span></div><div class="HOEnZb"><div class="h5"><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 text="#000000" bgcolor="#FFFFFF">
<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_8253614111703789905m_7859209184321000958moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
</span><div><div class="m_8253614111703789905h5"><div class="m_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_8253614111703789905m_7859209184321000958HOEnZb">
<div class="m_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 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">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_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459moz-signature" cols="72">Laurent</pre>
<div>
<div class="m_8253614111703789905m_7859209184321000958m_2482960030529164216h5">
<div class="m_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_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459HOEnZb">
<div class="m_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 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_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696m_-4724915924681828514moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div>
<div class="m_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696h5">
<div class="m_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_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_8253614111703789905m_7859209184321000958m_2482960030529164216m_-6995096064473700459m_5520331521785988696m_-4724915924681828514mimeAttachmentHeader"></fieldset>
<br>
</div>
</div>
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</pre>
</blockquote>
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</blockquote>
</div>
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</blockquote>
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</blockquote>
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</div></div></blockquote></div><br></div>