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<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
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Could the check be done using dbSNP rs as matching identifier?<br>
I mean OMIM phenotype feature has "rs", can this be retrieved from
tva also to match them?<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 17/08/15 13:16, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX3aj5rNW=NAzWxYeFZPuaRet3Y+PZnAuPGbJzVJL0Fc+g@mail.gmail.com"
type="cite">
<p dir="ltr">Yes, I'm afraid that's one of the consequences of
OMIM being a manually curated resource - you have to scan the
OMIM page by eye to find that sort of detail. </p>
<p dir="ltr">Will</p>
<div class="gmail_quote">On 17 Aug 2015 12:09, "Guillermo Marco
Puche" <<a moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Hi Will,<br>
<br>
Awesome! ClinVar is so direct to check $tva->feature_seq
with $pf->risk_allele.<br>
<br>
As you said, for other PhenotypeFeatures like OMIM there's
no risk_allele, allele_symbol or allele_accession_id.<br>
<br>
<b>1 2228866 rs387907306 G A,T<br>
<br>
</b>For this case I'm getting two OMIM phenotype features I
can't "check" if correct since risk_allele association
provides the OMIM allelic variant number<b>. </b>I guess
then there's no way to associate OMIM phenotype feature to a
specific allele.<br>
<b><br>
</b>
<blockquote><b><b># omim_feature: 1</b></b><br>
<b><b> </b></b>phenotype_description: Shprintzen-Goldberg
craniosynostosis syndrome<br>
source_name: OMIM<br>
external_reference: MIM:164780<br>
is_significant: 1<br>
variation allele: A<br>
The risk allele is: 0004<br>
</blockquote>
<b><b> </b></b>
<blockquote><b><b> # omim_feature: 2</b></b><br>
<b><b> </b></b>phenotype_description: Shprintzen-Goldberg
craniosynostosis syndrome<br>
source_name: OMIM<br>
external_reference: MIM:164780<br>
is_significant: 1<br>
variation allele: A<br>
The risk allele is: 0005<br>
<br>
<b> # omim_feature: 1</b><br>
<b> </b>phenotype_description: Shprintzen-Goldberg
craniosynostosis syndrome<br>
source_name: OMIM<br>
external_reference: MIM:164780<br>
is_significant: 1<br>
variation allele: T<br>
The risk allele is: 0004<br>
<b> </b><br>
<b> # omim_feature: 2</b><br>
<b> </b>phenotype_description: Shprintzen-Goldberg
craniosynostosis syndrome<br>
source_name: OMIM<br>
external_reference: MIM:164780<br>
is_significant: 1<br>
variation allele: T<br>
The risk allele is: 0005<br>
</blockquote>
<br>
<br>
Regards,<br>
Guillermo.<br>
<b> </b><br>
<div>On 17/08/15 10:25, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>The plugin run() sub-routine is executed for each
allele + transcript combination; the object is a
TranscriptVariationAllele, and you can find to which
allele you are referring with either
$tva->variation_feature_seq() or
$tva->feature_seq(); these give you the allele
relative to the input variant and transcript
respectively (i.e. the two will differ if the
transcript is on the reverse strand. See <a
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1TranscriptVariationAllele.html"
target="_blank">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1TranscriptVariationAllele.html</a></div>
<div><br>
</div>
<div>The data you return from the run() sub will only
appear in the block of output for that allele.</div>
<div><br>
</div>
<div>If you are retrieving phenotype data from Ensembl,
then you may find that we don't always have an
allele-specific annotation stored. For some
PhenotypeFeature objects, they will have an attribute
"risk_allele", "allele_accession_id" or
"allele_symbol", but many will not. You may also find
that due to strand or reporting issues, the sequence
in the associated allele may not match exactly one of
the alleles from the VariationFeature or VCF.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 14 August 2015 at 14:49,
Guillermo Marco Puche <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Dear devs,<br>
<br>
I would like to know what's the correct way to
handle information when multiple alleles appear in
a VCF record.<br>
<br>
For example,
Homo_sapiens_clinically_associated.vcf dataset:<br>
<br>
<b>1 2228866 rs387907306 G A,T</b><br>
<br>
Each one of alternative alleles has different OMIM
and Clinvar allele info.<br>
<br>
The plugin code is using the following scope:<br>
<br>
<b>sub feature_types {</b><b><br>
</b><b> return ['Transcript'];</b><b><br>
</b><b>}<br>
<br>
</b>Is there another feature_type level like
Transcript, Allele?<b><br>
</b><br>
I'm trying to solve it with the iteration code you
provided me Will:<span><br>
<br>
<b> foreach my
$known_var(@{$vf->{existing} || []}) {</b><b><br>
</b><b> foreach my
$pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})}){</b><b><br>
</b></span><b> #do_stuff</b><b><br>
</b><b> }</b><b><br>
</b><b>}</b><br>
<br>
However this is getting me the phenotype
information for both alternative alleles (A and T)
(transcript level) and this being wrote in output
for every alternative allele consequence twice. So
I'm getting phenotype info of A,T written in
allele A consequences and in allele T
consequences.<br>
<br>
How can I get the phenotype informartion for each
allele sperately? I think Ensembl can handle this
since in VCF output consequences are separated not
only by transcript but also by alternative allele.<br>
<br>
Thank you,<br>
<br>
Best regards,<br>
Guillermo.
<div>
<div><br>
<br>
<br>
<div>On 26/03/15 12:57, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">You will probably see odd
behaviour if you mix versions of the
script / API / caches / databases. Feel
free to experiment, though we can't
support such setups obviously.
<div><br>
</div>
<div>It works fine for me on 75 or 79
(i.e. using "git checkout --release 75"
in ensembl-tools, ensembl-variation,
ensembl-core)</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 26 March 2015
at 11:26, Guillermo Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF">
I guess it's a problem with my API
installation then.<br>
<br>
If I install latest API(79) and
continue to use <a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a>
from version 75 will it continue
working or I'll get conflicts/weird
behaviours?<br>
<br>
Thanks!<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<br>
<div>On 26/03/15 11:53, Will
McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Example output
(I set
$Data::Dumper::Maxdepth =
1;):
<div><br>
</div>
<div>> echo "rs699" |
perl -I
~/Git/guillermo/vep/ <a
moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a>
-plugin Clinvar -data
-force -db 75<br>
</div>
<div>
<div>2015-03-26 10:51:38 -
Reading input from STDIN
(or maybe you forgot to
specify an input
file?)...</div>
<div>2015-03-26 10:51:38 -
Starting...</div>
<div>2015-03-26 10:51:38 -
Detected format of input
file as id</div>
<div>2015-03-26 10:51:38 -
Read 1 variants into
buffer</div>
<div>2015-03-26 10:51:38 -
Checking for existing
variations</div>
<div>[===================================================================================================================================================================================================]
[ 100% ]</div>
<div>2015-03-26 10:51:38 -
Reading transcript data
from cache and/or
database</div>
<div>[===================================================================================================================================================================================================]
[ 100% ]</div>
<div>2015-03-26 10:51:38 -
Retrieved 4 transcripts
(0 mem, 0 cached, 4 DB,
0 duplicates)</div>
<div>2015-03-26 10:51:38 -
Analyzing chromosome 1</div>
<div>2015-03-26 10:51:38 -
Analyzing variants</div>
<div>[===================================================================================================================================================================================================]
[ 100% ]</div>
</div>
<div>
<div>2015-03-26 10:51:38 -
Calculating consequences</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '2853',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'HYPERTENSION,
ESSENTIAL,
SUSCEPTIBILITY TO'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '20384',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'Susceptibility_to_progression_to_renal_failure_in_IgA_nephropathy'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '20369',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'Preeclampsia,_susceptibility_to'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '26451',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'HYPERTENSION,_ESSENTIAL,_SUSCEPTIBILITY_TO'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '1',</div>
<div>
'name' =>
'HGMD_MUTATION',</div>
<div>
'description' =>
'Annotated by HGMD but
no phenotype description
is publicly available'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '6522',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'COSMIC:tumour_site:large_intestine'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '6529',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'COSMIC:tumour_site:breast'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '2853',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'HYPERTENSION,
ESSENTIAL,
SUSCEPTIBILITY TO'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '20384',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'Susceptibility_to_progression_to_renal_failure_in_IgA_nephropathy'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '20369',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'Preeclampsia,_susceptibility_to'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '26451',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'HYPERTENSION,_ESSENTIAL,_SUSCEPTIBILITY_TO'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '1',</div>
<div>
'name' =>
'HGMD_MUTATION',</div>
<div>
'description' =>
'Annotated by HGMD but
no phenotype description
is publicly available'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '6522',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'COSMIC:tumour_site:large_intestine'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>$VAR1 = bless( {</div>
<div>
'adaptor' =>
'Bio::EnsEMBL::Variation::DBSQL::PhenotypeAdaptor=HASH(0x43c39a8)',</div>
<div>
'dbID' => '6529',</div>
<div>
'name' => undef,</div>
<div>
'description' =>
'COSMIC:tumour_site:breast'</div>
<div> },
'Bio::EnsEMBL::Variation::Phenotype'
);</div>
<div>2015-03-26 10:51:38 -
Processed 1 total
variants (1 vars/sec, 1
vars/sec total)</div>
<div>2015-03-26 10:51:38 -
Wrote stats summary to
variant_effect_output.txt_summary.html</div>
<div>2015-03-26 10:51:38 -
Finished!</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On
26 March 2015 at 10:43,
Guillermo Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div text="#000066"
bgcolor="#FFFFFF">
Hello Will,<br>
<br>
I already had enabled
"check_existing" on my
VEP config template,
however I followed
your advice and
updated code to force
in the new() method
with your code.<br>
I'm still getting no
prints of line 64:<br>
<span><br>
print</span><span>
Dumper(</span><span>$pf</span><span>-></span><span>phenotype());<br>
</span><br>
Are you getting any
output printed? As I
said I get no errors
but nothing is printed
neither. This data
dumper should be
printing result of
phenotype() method
call.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<br>
<div>On 26/03/15
11:05, Will
McLaren wrote:<br>
</div>
<blockquote
type="cite">
<div dir="ltr">I
think perhaps
you haven't
enabled
--check_existing;
this is
required for
$vf->{existing}
to get
populated.<br>
<div><br>
</div>
<div>You can
force it on in
the new()
method of your
plugin:</div>
<div><br>
</div>
<div>$self->{config}->{check_existing}
= 1;</div>
<div><br>
</div>
<div>It then
works for me
on release/75
and
release/79.</div>
<div><br>
</div>
<div>Will</div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
25 March 2015
at 17:35,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div
text="#000066"
bgcolor="#FFFFFF"> Hello Will,<br>
<br>
With your
explanations
I'm trying to
call phenotype
(as you said I
was accessing
the hashref
directly).<br>
I'm using
input set you
linked.
However my
local Ensembl
installation
is v75.<br>
<br>
This is the
code of the
plugin:<br>
<a
moz-do-not-send="true"
href="https://github.com/guillermomarco/vep/blob/master/Clinvar.pm"
target="_blank">https://github.com/guillermomarco/vep/blob/master/Clinvar.pm</a><br>
<br>
I'm getting
absolutelty no
info nor
errors. I've
no idea if
this is an
issue with my
database/API
version or
with the
plugin code
itself.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<br>
<div>On
16/03/15
17:50, Will
McLaren wrote:<br>
</div>
<blockquote
type="cite">
<div dir="ltr">The
"is_significant"
field is an
internal flag
that doesn't
necessarily
have the
meaning you
expect; it is
used to
distinguish
between
genuine
reported
associations
and e.g.
non-significant
associations
reported from
genome-wide
studies.
<div><br>
</div>
<div>You
should not see
undef for
phenotype; I
suspect you
are accessing
the hashref
directly
($pf->{phenotype})
rather than
making the
method call
($pf->phenotype()).</div>
<div><br>
</div>
<div>You could
try <a
moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/release-79/variation/vcf/homo_sapiens/Homo_sapiens_clinically_associated.vcf.gz"
target="_blank">ftp://ftp.ensembl.org/pub/release-79/variation/vcf/homo_sapiens/Homo_sapiens_clinically_associated.vcf.gz</a>
as a test
input set.</div>
<div><br>
</div>
<div>Will</div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
16 March 2015
at 16:39,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote">
<div> Hi Will,<br>
<br>
Thank you for
your quick
response! Very
clarifying.<br>
<br>
I guess that
the way to
retrieve
ClinVar data I
posted is
correct. With
my test
dataset I've
only seen
"is_significant"
values of "1"
and undef
'phenotype'
values. I
think I need a
synthetic vcf
with ClinVar
annotation
variants to
very that the
plugin is
working.<br>
<br>
I've been
looking on
Ensembl
website for a
test dataset.
I think you
don't provide
any right?
Correct me if
I'm wrong.<br>
<br>
Thanks!<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<div>On
16/03/15
16:16, Will
McLaren wrote:<br>
</div>
<blockquote
type="cite">
<div dir="ltr">Hi
Guillermo,
<div><br>
</div>
<div>To get
the rest of
that data in
the table you
need to access
the additional
attributes of
the
PhenotypeFeature
object,
something
like:</div>
<div><br>
</div>
<div>my $attr
=
$pfs->[0]->get_all_attributes;<br>
</div>
<div>print
"$_:".$attr->{$_}."\t"
for keys
%$attr;</div>
<div>print
"\n;</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
<div><br>
</div>
<div>More
info: the
reason these
data are
stored as
attributes is
due to the
diverse data
sources and
types that we
import into
our phenotype
schema; to
create a
database
column and
corresponding
API method for
each data type
(p-value,
review status,
risk allele,
external ID
etc etc) would
be cumbersome
and
inefficient.
To this end we
provide a few
methods that
shortcut the
attribute
approach for
the most
common data
types;
everything
else must be
accessed
through the
attributes
method. This
is a common
theme across
the Ensembl
API.</div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
13 March 2015
at 12:03,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote">
<div> Hi,<br>
<br>
I'm trying to
retrieve
ClinVar
information
with the code
example you
provided.<span><br>
<br>
my $self =
shift;<br>
my $tva =
shift;<br>
my $vf =
$tva->variation_feature;<br>
my $pfa =
$self->{config}->{reg}->get_adaptor('human','variation','phenotypefeature');<br>
<br>
foreach my
$known_var(@{$vf->{existing}
|| []}) {<br>
foreach my
$pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})})
{<br>
</span>
if
($pf->{'source'}
eq
"dbSNP_ClinVar"){<br>
print
"$pf->{'source'}\t$pf->{'external_id'}\t$pf->{'is_significant'}\t$pf->{'phenotype'}\n",
;<br>
}<br>
}<br>
}<br>
<br>
As you can see
I'm
"filtering"
the results to
only output
phenotype
feature when
source is
dbSNP_ClinVar.
I don't know
why but I
guess
filtering
should be done
when doing the
"fetch_all".<br>
<br>
On the other
hand I'm
trying to
retrieve
Disease,
Source and
Clinical
Significance
from this
example table:
<a
moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;r=8:19955518-19956518;v=rs268;vdb=variation;vf=266"
target="_blank">http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;r=8:19955518-19956518;v=rs268;vdb=variation;vf=266</a><br>
<br>
I think I'm
doing
something
wrong I got
totally lost
in
Phenotypefeature.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<div>On
02/03/15
16:05, Will
McLaren wrote:<br>
</div>
<blockquote
type="cite">
<div dir="ltr">If
you enable the
--check_existing
flag when you
run the VEP,
you'll be able
to see any
known
co-located
variants
attached to
the
VariationFeature
object in your
plugin:
<div><br>
</div>
<div>sub run {</div>
my $self =
shift;
<div> my $tva
= shift;</div>
<div> my $vf
=
$tva->variation_feature;</div>
<div><br>
</div>
<div> foreach
my
$known_var(@{$vf->{existing}
|| []}) {</div>
<div> # do
stuff</div>
<div> }</div>
<div>}</div>
<div><br>
</div>
<div>The
$known_var is
not an API
object but a
simple hashref
with a number
of fields;
you're
probably
interested in
$known_var->{clin_sig}</div>
<div><br>
</div>
<div>However,
as I
mentioned,
this is the
only data that
is stored in
the cache. To
access the
rating and the
specific
disease
association,
you'll need to
make calls to
the database
by getting an
adaptor,
something
like:</div>
<div><br>
</div>
<div>
<div>sub run {</div>
<div> my
$self = shift;</div>
<div> my $tva
= shift;</div>
<div> my $vf
=
$tva->variation_feature;</div>
<div> my $pfa
=
$self->{config}->{reg}->get_adaptor('human','variation','phenotypefeature');</div>
<div><br>
</div>
<div> foreach
my
$known_var(@{$vf->{existing}
|| []}) {</div>
<div>
foreach my
$pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})})
{</div>
<div> #
do stuff</div>
<div> }</div>
<div> }</div>
<div>}</div>
</div>
<div><br>
</div>
<div>Be aware
that this will
access the
database, so
unless you
have a local
copy please
don't run this
sort of code
on genome-wide
VCFs using our
public DB
server.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
2 March 2015
at 14:47,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote">
<div> Hi Will,<br>
<br>
Indeed I'm
looking to
retrieve this
information
from VEP
plugin.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<div>On
02/03/15
15:25, Will
McLaren wrote:<br>
</div>
<blockquote
type="cite">
<div dir="ltr">Hi
Guillermo,
<div><br>
</div>
<div>The
detailed
ClinVar
information is
stored against
PhenotypeFeature
objects (each
SNP/disease
pairing gets
its own entry
in ClinVar,
e.g. <a
moz-do-not-send="true"
href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2"
target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2</a>, <a
moz-do-not-send="true"
href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/"
target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/</a>, <a
moz-do-not-send="true"
href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/"
target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/</a>
for rs699).</div>
<div><br>
</div>
<div>The
rating (and
indeed the
clinical
significance)
is stored as
an attribute
on the
PhenotypeFeature
object; you
can retrieve
this with the
get_all_attributes()
method.</div>
<div><br>
</div>
<div>See <a
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html"
target="_blank">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html</a>
and <a
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype"
target="_blank">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype</a>
for more info.</div>
<div><br>
</div>
<div><span>Bio::EnsEMBL::Variation::</span><span>Utils::VEP::get_clin_sig()
is an internal
method that
you should not
use.</span></div>
<div><span><br>
</span></div>
<div><span>The
VEP cache
contains the
list of
clinical
significance
states for
each variant,
but neither
the disease
association or
the rating. If
you want help
getting access
to this data
via a plugin,
let me know as
it's a little
more involved
than the API
methods above
(though it is
faster as no
database
access is
required).</span><br>
</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will
McLaren</div>
<div>Ensembl
Variation</div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
2 March 2015
at 14:06,
Guillermo
Marco Puche <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote">
<div> Dear
devs,<br>
<br>
I'm looking
forward to
retrieve
ClinVar
information
and add it to
VEP
annotation.
From my
understanding
I should be
able to
retrieve
"Clinical
significance"
and "ClinVar
Rating".<br>
<br>
I've been
looking the
Varation API,
and I'm
confused. I
guess for
significance I
should use
Bio::EnsEMBL::Variation::Utils::VEP::get_clin_sig()
or
Bio::EnsEMBL::Variation::VariationFeature::get_all_clinical_significance_states().<br>
<br>
What about
ClinVar
rating? Is it
possible to
retrieve it
from API?<br>
<br>
Thanks!<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<br>
</div>
<br>
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