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<div class="moz-cite-prefix"><br>
Thanks for the clarification will,<br>
much appreciated!<br>
Cheers<br>
Seb<br>
<br>
<br>
<br>
On 06/02/13 20:36, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX0Vpza7CoTMMxbuYNzqNf5z=ZPUkEgvpxGiBQntZi4cig@mail.gmail.com"
type="cite">
<div dir="ltr">Hello Seb,
<div><br>
</div>
<div style="">Apologies if this is a little confusing.</div>
<div style=""><br>
</div>
<div style="">The --refseq flag only applies when you are using
the VEP with a database (public or local). It asks the VEP to
use the *_otherfeatures_* database instead of the *_core_*
database; this contains RefSeq transcripts rather than ENST
Ensembl transcripts.</div>
<div style=""><br>
</div>
<div style="">We provide the <span
style="font-size:13px;font-family:arial,sans-serif">homo_sapiens_refseq_vep_70.</span><span
style="font-size:13px;font-family:arial,sans-serif">ta</span><span
style="font-size:13px;font-family:arial,sans-serif">r.gz so
that you can get these same annotations in --offline or
--cache mode. To use this, you do not need to (and should
not) use --refseq, you should merely point to the directory
containing the unpacked cache using --dir.</span></div>
<div style=""><span
style="font-size:13px;font-family:arial,sans-serif"><br>
</span></div>
<div style=""><span
style="font-family:arial,sans-serif;font-size:13px">homo_sapiens_refseq_vep_70.</span><span
style="font-family:arial,sans-serif;font-size:13px">ta</span><span
style="font-family:arial,sans-serif;font-size:13px">r.gz has
some limitations, one of which is that it does not contain
HGNC identifiers for genes, hence why --hgnc does not work
for you in this situation. Unfortunately these mappings
between RefSeq and HGNC are somewhat hard to retrieve in
Ensembl due to the way that our Xref (external reference)
schema is put together. It is possible to retrieve these
mappings from other resources, for example the UCSC MySQL
server, and from there you could add this annotation to your
VEP output.</span><span
style="font-size:13px;font-family:arial,sans-serif"><br>
</span></div>
<div style=""><span
style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div style=""><span
style="font-family:arial,sans-serif;font-size:13px">Hope
this helps!</span></div>
<div style=""><span
style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div style=""><span
style="font-family:arial,sans-serif;font-size:13px">Regards</span></div>
<div style=""><span
style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div style=""><span
style="font-family:arial,sans-serif;font-size:13px">Will
McLaren</span></div>
<div style=""><span
style="font-family:arial,sans-serif;font-size:13px">Ensembl
Variation</span></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 6 February 2013 04:29, NextGenSeb <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:nextgenseb@gmail.com" target="_blank">nextgenseb@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
Dear all,<br>
<br>
I recently came across your variant effect predictor, so
first of all<br>
thanks for making that available, great tool!<br>
I have a few questions however pertaining to the --refseq
and --hgnc flags.<br>
<br>
First of all for the --refseq flag:<br>
<br>
After downloading both the homo_sapiens_refseq_vep_70.tar.gz<br>
homo_sapiens_vep_70.tar.gz caches from your ftp site and
putting them<br>
into /Data/VEP/homo_sapiens_refseq and
/Data/VEP/homo_sapiens folders,<br>
respectively, I tried the following two scenarios:<br>
<br>
perl<br>
/usr/bioinf/source/variant_effect_predictor/<a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a><br>
-i ./test.short.vcf --format vcf -o test.vep --verbose
--force_overwrite<br>
--refseq --cache --dir /Data/VEP/ --offline --everything
--species<br>
homo_sapiens<br>
<br>
perl<br>
/usr/bioinf/source/variant_effect_predictor/<a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a><br>
-i ./test.short.vcf --format vcf -o test.vep --verbose
--force_overwrite<br>
--refseq --cache --dir /Data/VEP/ --offline --everything
--species<br>
homo_sapiens_refseq<br>
<br>
Both commands ran without error, however neither
incorporated the refseq<br>
annotation in the output. Only when deleting both caches
again and<br>
unpacking homo_sapiens_refseq_vep_70.tar.gz into
/Data/VEP/homo_sapiens<br>
did the refseq NM_ tags get incorporated, but then even with
--refseq<br>
not set. This behavior did not change when removing the
--offline or<br>
the --everything flag.<br>
<br>
In principle that would be fine, however the -hgnc flag
appears to only<br>
work with the homo_sapiens_vep_70.tar.gz data set and not
the refseq<br>
one, again regardless of whether run in online or offline
mode.<br>
<br>
Now removing all cache files and running<br>
<br>
perl<br>
/usr/bioinf/source/variant_effect_predictor/<a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a><br>
-i ./test.short.vcf --format vcf -o test.vep --verbose
--force_overwrite<br>
--refseq --cache --dir /Data/VEP/ --write_cache --species
homo_sapiens<br>
<br>
does actually give the correct output. However in this case
adding the<br>
--everything flag not only will put a huge strain on the
server<br>
connection when using bigger datasets then my current test
one, but also<br>
throws an exception (see end of email). Hence I would rather
work of an<br>
offline cache. Could you please advise me whether there is a
way to fix<br>
this issue?<br>
<br>
Thanks in advance for your help,<br>
Cheers<br>
Seb<br>
<br>
<br>
<br>
perl<br>
/usr/bioinf/source/variant_effect_predictor/<a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a><br>
-i ./test.short.vcf --format vcf -o test.vep --verbose
--force_overwrite<br>
--refseq --cache --dir /Data/VEP/test --write_cache
--everything<br>
--species homo_sapiens --host <a moz-do-not-send="true"
href="http://useastdb.ensembl.org" target="_blank">useastdb.ensembl.org</a><br>
<br>
#----------------------------------#<br>
# ENSEMBL VARIANT EFFECT PREDICTOR #<br>
#----------------------------------#<br>
<br>
version 2.8<br>
<br>
By Will McLaren (<a moz-do-not-send="true"
href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)<br>
<br>
Configuration options:<br>
<br>
cache 1<br>
canonical 1<br>
ccds 1<br>
core_type otherfeatures<br>
dir /Data/VEP/test<br>
domains 1<br>
everything 1<br>
force_overwrite 1<br>
format vcf<br>
gmaf 1<br>
hgnc 1<br>
hgvs 1<br>
host <a moz-do-not-send="true"
href="http://useastdb.ensembl.org" target="_blank">useastdb.ensembl.org</a><br>
input_file ./test.short.vcf<br>
numbers 1<br>
output_file test.vep<br>
polyphen b<br>
port 5306<br>
protein 1<br>
refseq 1<br>
regulatory 1<br>
sift b<br>
species homo_sapiens<br>
toplevel_dir /Data/VEP/test<br>
verbose 1<br>
write_cache 1<br>
<br>
--------------------<br>
<br>
<br>
<br>
Will only load v70 databases<br>
Species 'homo_sapiens' loaded from database
'homo_sapiens_core_70_37'<br>
Species 'homo_sapiens' loaded from database
'homo_sapiens_cdna_70_37'<br>
Species 'homo_sapiens' loaded from database
'homo_sapiens_vega_70_37'<br>
Species 'homo_sapiens' loaded from database<br>
'homo_sapiens_otherfeatures_70_37'<br>
Species 'homo_sapiens' loaded from database
'homo_sapiens_rnaseq_70_37'<br>
homo_sapiens_variation_70_37 loaded<br>
homo_sapiens_funcgen_70_37 loaded<br>
Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so the
following<br>
compara databases will be ignored: ensembl_compara_70<br>
ensembl_ancestral_70 loaded<br>
ensembl_ontology_70 loaded<br>
ensembl_stable_ids_70 loaded<br>
2013-02-06 11:21:35 - Connected to core version 70 database
and<br>
variation version 70 database<br>
2013-02-06 11:21:35 - INFO: Cache directory<br>
/Data/VEP/test/homo_sapiens/70 not found - it will be
created<br>
2013-02-06 11:21:40 - INFO: Database will be accessed when
using --hgvs<br>
2013-02-06 11:21:40 - INFO: Database will be accessed when
using --sift;<br>
consider using the complete cache containing sift data (see<br>
documentation for details)<br>
2013-02-06 11:21:40 - INFO: Database will be accessed when
using<br>
--polyphen; consider using the complete cache containing
polyphen data<br>
(see documentation for details)<br>
2013-02-06 11:21:40 - INFO: Database will be accessed when
using<br>
--regulatory; consider using the complete cache containing
regulatory<br>
data (see documentation for details)<br>
2013-02-06 11:21:40 - Starting...<br>
2013-02-06 11:21:42 - Read 62 variants into buffer<br>
2013-02-06 11:21:42 - Reading transcript data from cache
and/or database<br>
[======================================================================================================]<br>
[ 100% ]<br>
2013-02-06 12:01:12 - Retrieved 409 transcripts (0 mem, 0
cached, 411<br>
DB, 2 duplicates)<br>
2013-02-06 12:01:12 - Reading regulatory data from cache
and/or database<br>
[======================================================================================================]<br>
[ 100% ]<br>
2013-02-06 12:05:08 - Retrieved 1738 regulatory features (0
mem, 0<br>
cached, 1738 DB, 0 duplicates)<br>
2013-02-06 12:05:08 - Checking for existing variations<br>
[======================================================================================================]<br>
[ 100% ]<br>
2013-02-06 12:05:33 - Analyzing chromosome 1<br>
2013-02-06 12:05:33 - Analyzing variants<br>
[======================================================================================================]<br>
[ 100% ]<br>
2013-02-06 12:05:33 - Analyzing RegulatoryFeatures<br>
[======================================================================================================]<br>
[ 100% ]<br>
2013-02-06 12:05:33 - Analyzing MotifFeatures<br>
[======================================================================================================]<br>
[ 100% ]<br>
2013-02-06 12:05:33 - Calculating consequences<br>
[=======> ] [ 9% ]<br>
-------------------- EXCEPTION --------------------<br>
MSG: Got to have an Exon object, not a<br>
STACK Bio::EnsEMBL::Translation::start_Exon<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Translation.pm:271<br>
STACK Bio::EnsEMBL::Transcript::transfer<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Transcript.pm:2511<br>
STACK Bio::EnsEMBL::Variation::BaseTranscriptVariation::_three_prime_utr<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Variation/BaseTranscriptVariation.pm:638<br>
STACK<br>
Bio::EnsEMBL::Variation::TranscriptVariationAllele::_get_alternate_cds<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm:1169<br>
STACK<br>
Bio::EnsEMBL::Variation::TranscriptVariationAllele::_get_fs_peptides<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm:1090<br>
STACK<br>
Bio::EnsEMBL::Variation::TranscriptVariationAllele::_get_hgvs_peptides<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm:930<br>
STACK Bio::EnsEMBL::Variation::TranscriptVariationAllele::hgvs_protein<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm:705<br>
STACK Bio::EnsEMBL::Variation::Utils::VEP::tva_to_line<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1639<br>
STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_to_consequences<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1472<br>
STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_list_to_cons<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1275<br>
STACK Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences<br>
/usr/bioinf/source/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1056<br>
STACK main::main<br>
/usr/bioinf/source/variant_effect_predictor/<a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl:270"
target="_blank">variant_effect_predictor.pl:270</a><br>
STACK toplevel<br>
/usr/bioinf/source/variant_effect_predictor/<a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl:116"
target="_blank">variant_effect_predictor.pl:116</a><br>
Date (localtime) = Wed Feb 6 12:05:33 2013<br>
Ensembl API version = 70<br>
---------------------------------------------------<br>
<br>
<br>
<br>
<br>
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</blockquote>
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