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<p>Dear Duarte,</p>
<p><br>
You can download the 1000 Genomes VCFs and their indexed files
here (it's quite big!): <span class="pl-s"><span class="pl-pds"></span>f<a
moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/">tp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/ALL.chr...</a></span><br>
</p>
<p><br>
Then you need to edit the following file in your Ensembl Variation
API
(ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json):</p>
<a moz-do-not-send="true"
href="https://github.com/Ensembl/ensembl-variation/blob/release/95/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json#L20-L22">https://github.com/Ensembl/ensembl-variation/blob/release/95/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json#L20-L22</a>
<p>And replace the highlighted lines by:<br>
<br>
"type": "local",<br>
"strict_name_match": 1,<br>
"filename_template":
"<path_to_the_directory_where_you_downloaded_the_vcf_files>/ALL.chr###CHR###_GRCh38.genotypes.20170504.vcf.gz",</p>
<p><br>
Best regards,<br>
</p>
<pre class="moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div class="moz-cite-prefix">On 18/01/2019 14:32, Duarte Molha
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAGqkoELtTGA0gpDVo1Fr4n3PNaRFwE+TPe15KUCJO4B-i8pHMQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Just another question
<div><br>
</div>
<div>I can do what you say by querying the ensembl database
remotely. But we have installed it locally as well and since
my queries would be extensive I much prefered if I could also
to this locally.</div>
<div><br>
</div>
<div>Where and how do I download the VCFs and install them on my
own server so that this can also be done locally?</div>
<div><br>
</div>
<div>Many thanks</div>
<div>Duarte</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, 17 Jan 2019 at 11:28,
Laurent Gil <<a href="mailto:lgil@ebi.ac.uk"
moz-do-not-send="true">lgil@ebi.ac.uk</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Dear Duarte,<br>
<br>
The 1000 Genomes Phase 3 data are stored in a VCF file and
not in a database (it was too big to store it in our
databases), that's why you didn't see them in your
results.<br>
However you can access it with the Ensembl Variation API.
For that, you need add the following line in your script
to force the API to look into the Ensembl Variation VCF
files:<br>
</p>
<pre>$variation_adaptor->db->use_vcf(1);</pre>
<p><br>
Here is a suggestion of your script with the change:<br>
</p>
<pre class="gmail-m_-121412223426997746code gmail-m_-121412223426997746sh_perl gmail-m_-121412223426997746sh_sourceCode"><span class="gmail-m_-121412223426997746sh_keyword">my</span> <span class="gmail-m_-121412223426997746sh_variable">$variation_adaptor</span> <span class="gmail-m_-121412223426997746sh_symbol">=</span> <span class="gmail-m_-121412223426997746sh_variable">$registry</span><span class="gmail-m_-121412223426997746sh_symbol">-></span><span class="gmail-m_-121412223426997746sh_function">get_adaptor</span><span class="gmail-m_-121412223426997746sh_symbol">(</span><span class="gmail-m_-121412223426997746sh_string">"human"</span><span class="gmail-m_-121412223426997746sh_symbol">,</span> <span class="gmail-m_-121412223426997746sh_string">"variation"</span><span class="gmail-m_-121412223426997746sh_symbol">,</span> <span class="gmail-m_-121412223426997746sh_string">"variation"</span><span class="gmail-m_-121412223426997746sh_symbol">);
</span>
<span class="gmail-m_-121412223426997746sh_symbol">$variation_adaptor->db->use_vcf(1);</span></pre>
<pre>my $variation = $variation_adaptor->fetch_by_name($id);</pre>
<div>
<pre>foreach my $vf (@{$variation->get_all_VariationFeatures()}) {</pre>
<pre> ...</pre>
<pre>}</pre>
</div>
<p>Note that I also replaced the VariationFeatureAdaptor
call "$vf_adaptor->fetch_all_by_Variation($var)}" to
avoid using/instantiate an extra adaptor.</p>
<p>There are some further descriptions in our Ensembl
Variation API tutorial: <a
href="https://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles"
target="_blank" moz-do-not-send="true">https://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles</a></p>
<p><br>
</p>
<p>Best regards,<br>
</p>
<pre class="gmail-m_-121412223426997746moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div class="gmail-m_-121412223426997746moz-cite-prefix">On
17/01/2019 09:54, Duarte Molha wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr"
class="gmail-m_-121412223426997746gmail_signature">
<div>Dear Developers </div>
<div><br>
</div>
<div>I created a simple script to
provide me with polymorphic
frequencies in the different
populations in the database. However
after running it on my set it seems
some variations do not show results</div>
<div><br>
</div>
<div><br>
</div>
take for example the INDEL rs141080692
<div> </div>
<div>When I run it though my script
this is the information I get:</div>
<div><br>
</div>
<div>
<div>rs141080692 GT
1000GENOMES:pilot_1_CEU_low_coverage_panel
- deletion 9
123543905 123543907</div>
<div>rs141080692 -
1000GENOMES:pilot_1_CEU_low_coverage_panel
- deletion 9
123543905 123543907</div>
<div>rs141080692 GT
1000GENOMES:pilot_1_CHB+JPT_low_coverage_panel
- deletion 9
123543905 123543907</div>
<div>rs141080692 -
1000GENOMES:pilot_1_CHB+JPT_low_coverage_panel
- deletion 9
123543905 123543907</div>
<div>rs141080692 GT
1000GENOMES:pilot_1_YRI_low_coverage_panel
- deletion 9
123543905 123543907</div>
<div>rs141080692 -
1000GENOMES:pilot_1_YRI_low_coverage_panel
- deletion 9
123543905 123543907</div>
<div>rs141080692 GT
GMI:AK_Koreans - deletion
9 123543905
123543907</div>
<div>rs141080692 -
GMI:AK_Koreans - deletion
9 123543905
123543907</div>
<div>rs141080692 GT
GMI:NA10851 - deletion
9 123543905
123543907</div>
<div>rs141080692 -
GMI:NA10851 - deletion
9 123543905
123543907</div>
<div>rs141080692 GT
SSMP:SSM - deletion
9 123543905
123543907</div>
<div>rs141080692 -
SSMP:SSM - deletion
9 123543905
123543907</div>
</div>
<div><br>
</div>
<div>however, looking at the same
database in your website:</div>
<div><br>
</div>
<div><a
href="http://dec2015.archive.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=9:123543406-123544407;v=rs141080692;vdb=variation;vf=127601209"
target="_blank"
moz-do-not-send="true">http://dec2015.archive.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=9:123543406-123544407;v=rs141080692;vdb=variation;vf=127601209</a><br>
</div>
<div><br>
</div>
<div>You can see that there is
information about its frequency in a
whole bunch of populations</div>
<div><br>
</div>
<div>How do I go about fetching these?</div>
<div><br>
</div>
<div>My script is pretty basic</div>
<div><br>
</div>
<div>first I fect all populations or
only ones I am interested in with:</div>
<div><br>
</div>
<div>
<div>foreach my $pop
(@{$population_adaptor->fetch_all()}){</div>
<div><span style="white-space:pre-wrap"> </span>my
$name = $pop->name();</div>
<div><span style="white-space:pre-wrap"> </span>if
(defined $name){</div>
<div><span style="white-space:pre-wrap"> </span>if
(defined $population){</div>
<div><span style="white-space:pre-wrap"> </span>if
($name =~ /\Q$population/){</div>
<div><span style="white-space:pre-wrap"> </span>print
STDERR "Selected Populations:
$name \n";</div>
<div><span style="white-space:pre-wrap"> </span>push
@selected_populations, $name; </div>
<div><span style="white-space:pre-wrap"> </span>}</div>
<div><span style="white-space:pre-wrap"> </span>}else{</div>
<div><span style="white-space:pre-wrap"> </span>print
STDERR "Selected Populations:
$name \n";</div>
<div><span style="white-space:pre-wrap"> </span>push
@selected_populations, $name; </div>
<div><span style="white-space:pre-wrap"> </span></div>
<div><span style="white-space:pre-wrap"> </span>}</div>
<div><span style="white-space:pre-wrap"> </span>}</div>
<div>}</div>
</div>
<div><br>
</div>
<div>I then use the variation adaptor
to get the variation object</div>
<div><br>
</div>
<div>
<div> my $variation =
$variation_adaptor->fetch_by_name($id);</div>
</div>
<div><br>
</div>
<div>Then I cycle though each
variation feature with </div>
<div><br>
</div>
<div>
<div>foreach my $vf
(@{$vf_adaptor->fetch_all_by_Variation($var)}){</div>
</div>
<div>
<div><span style="white-space:pre-wrap"> </span>my
@alleles =
@{$vf->get_all_Alleles};</div>
</div>
<div><br>
</div>
<div>
<div><span style="white-space:pre-wrap"> </span>ALLELE_CYCLE:foreach
my $a (@alleles){</div>
<div><span style="white-space:pre-wrap"> </span>my
$astr = $a->allele();</div>
<div><span style="white-space:pre-wrap"> </span>my
$pop = $a->population();</div>
<div><span style="white-space:pre-wrap"> </span>my
$pop_name = "-";</div>
<div><span style="white-space:pre-wrap"> </span>if
(defined $pop){</div>
<div><span style="white-space:pre-wrap"> </span>$pop_name
= $a->population->name() ;</div>
<div><span style="white-space:pre-wrap"> </span>}</div>
<div><span style="white-space:pre-wrap"> </span>my
$freq = $a->frequency() || "-";</div>
<div><span style="white-space:pre-wrap"> </span></div>
<div><span style="white-space:pre-wrap"> </span>foreach
my $p (@{$selected_populations}){</div>
<div><span style="white-space:pre-wrap"> </span>#print
STDERR $pop_name."\t".$p."\n";</div>
<div><span style="white-space:pre-wrap"> </span>if
($pop_name eq $p){</div>
<div><span style="white-space:pre-wrap"> </span>print
$out_fh join "\t", (<span style="white-space:pre-wrap"> </span>$var->name(),</div>
<div><span style="white-space:pre-wrap"> </span>$astr,</div>
<div><span style="white-space:pre-wrap"> </span>$pop_name,</div>
<div><span style="white-space:pre-wrap"> </span>$freq,</div>
<div><span style="white-space:pre-wrap"> </span>$varClass, </div>
<div><span style="white-space:pre-wrap"> </span>$chr, </div>
<div><span style="white-space:pre-wrap"> </span>$start, </div>
<div><span style="white-space:pre-wrap"> </span>$end."\n");</div>
<div><span style="white-space:pre-wrap"> </span>next
ALLELE_CYCLE;</div>
<div><span style="white-space:pre-wrap"> </span>}</div>
<div><span style="white-space:pre-wrap"> </span>}</div>
<div><span style="white-space:pre-wrap"> </span>}</div>
</div>
<div>}</div>
<div><br>
</div>
<div>Am I doing something wrong? </div>
<div>There are the phase3 population
data for example. They are clealy
included in your site</div>
<div><br>
</div>
<div>Many thanks</div>
<div><br>
</div>
<div>Duarte</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset
class="gmail-m_-121412223426997746mimeAttachmentHeader"></fieldset>
<pre class="gmail-m_-121412223426997746moz-quote-pre">_______________________________________________
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</pre>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
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