<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Johanne,<div class=""><br class=""></div><div class=""><div class="">The name for the European super population is 1000GENOMES:phase_3:EUR. You can use the name for fetching the population object like this:</div><div class=""><br class=""></div><div class="">my $ld_population = $pop_adaptor->fetch_by_name('1000GENOMES:phase_3:EUR');</div><div class=""><br class=""></div><div class="">However, the European super population contains 503 samples and exceeds the number of genotypes supported by our script for computing LD data. Therefore, you need to loop over all European populations and we will need to check if we can increase the number of allowed populations. This could become availabe in release 85 which is planned for summer.</div><div class=""><br class=""></div><div class="">MAG stands for Mandinka in The Gambia and is part of the African super population. The 1000 Genomes website is using the correct name which is GWD (Gambian in Western Divisions in the Gambia). We will move to using GWD in release 84. You can find a list of all 1000 Genomes phase 3 populations here: <a href="http://www.ensembl.org/info/genome/variation/data_description.html#populations" class="">http://www.ensembl.org/info/genome/variation/data_description.html#populations</a>.</div><div class=""><br class=""></div><div class="">It doesn't matter which adaptor you use to set the use_vcf flag. The flag is passed on to the DBAdaptor. All other adaptors will have access to the flag and check the value if needed.</div><div class=""><br class=""></div><div class="">You can set and update use_vcf accordingly: non-zero value instructs the API to look in configured VCF files for genotype-based data. Setting to 1 tells the API to use both the DB and VCF; setting to 2 tells the API to use only VCF.</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Anja</div><div class=""><br class=""></div><div><blockquote type="cite" class=""><div class="">On 28 Feb 2016, at 14:50, Johanne Håøy Horn <<a href="mailto:johannhh@ifi.uio.no" class="">johannhh@ifi.uio.no</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Dear Ensembl dev team,<br class="">
<div class="">
<div class=""><br class="">
</div>
<div class="">I try to see what populations are available from your ENSEMBL api, and with the following script I get the populations listed below:</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""><font face="Courier New" class="">use strict;</font></div>
<div class=""><font face="Courier New" class="">use warnings;</font></div>
<div class=""><font face="Courier New" class="">use Bio::EnsEMBL::Registry;</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">my $registry = 'Bio::EnsEMBL::Registry';</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">$registry->load_registry_from_db(</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>-host => '<a href="http://ensembldb.ensembl.org/" class="">ensembldb.ensembl.org</a>',</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>-user => 'anonymous'</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>);</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""># Connect to the databases:</font></div>
<div class=""><font face="Courier New" class="">my $variation_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'variation');</font></div>
<div class=""><font face="Courier New" class="">my $pop_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'population');</font></div>
<div class=""><font face="Courier New" class="">$variation_adaptor->db->use_vcf(1);</font></div>
<div class=""><font face="Courier New" class="">$pop_adaptor->db->use_vcf(1);</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""># Print out all available populations:</font></div>
<div class=""><font face="Courier New" class="">my $ld_populations = $pop_adaptor->fetch_all_LD_Populations();</font></div>
<div class=""><font face="Courier New" class="">foreach my $ld_pop (@$ld_populations) {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>print $ld_pop->name, "\n";</font></div>
<div class=""><font face="Courier New" class="">}</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">my $ld_population = $pop_adaptor->fetch_by_name('EUR');</font></div>
</div>
<div class=""><br class="">
</div>
<div class="">POPULATIONS:</div>
<div class="">
<div class="">1000GENOMES:phase_3:ACB</div>
<div class="">1000GENOMES:phase_3:ASW</div>
<div class="">1000GENOMES:phase_3:BEB</div>
<div class="">1000GENOMES:phase_3:CDX</div>
<div class="">1000GENOMES:phase_3:CEU</div>
<div class="">1000GENOMES:phase_3:CHB</div>
<div class="">1000GENOMES:phase_3:CHS</div>
<div class="">1000GENOMES:phase_3:CLM</div>
<div class="">1000GENOMES:phase_3:ESN</div>
<div class="">1000GENOMES:phase_3:FIN</div>
<div class="">1000GENOMES:phase_3:GBR</div>
<div class="">1000GENOMES:phase_3:GIH</div>
<div class="">1000GENOMES:phase_3:IBS</div>
<div class="">1000GENOMES:phase_3:ITU</div>
<div class="">1000GENOMES:phase_3:JPT</div>
<div class="">1000GENOMES:phase_3:KHV</div>
<div class="">1000GENOMES:phase_3:LWK</div>
<div class="">1000GENOMES:phase_3:MAG # <— This is the population I cannot find documentation for</div>
<div class="">1000GENOMES:phase_3:MSL</div>
<div class="">1000GENOMES:phase_3:MXL</div>
<div class="">1000GENOMES:phase_3:PEL</div>
<div class="">1000GENOMES:phase_3:PJL</div>
<div class="">1000GENOMES:phase_3:PUR</div>
<div class="">1000GENOMES:phase_3:STU</div>
<div class="">1000GENOMES:phase_3:TSI</div>
<div class="">1000GENOMES:phase_3:YRI</div>
</div>
<div class=""><br class="">
</div>
<div class="">This page explains the population codes: <a href="http://www.1000genomes.org/category/population/" class="">http://www.1000genomes.org/category/population/</a></div>
<div class="">However, I can’t find the extended version of the MAG abbreviation (marked above), not when searching elsewhere either. Which population is it, and what is its super population? </div>
<div class="">Also, do you have populations from other research initiatives than 1000G?</div>
<div class=""><br class="">
</div>
<div class="">I have also been wondering if I should tell all adaptors, that is LDFeatureContainerAdaptor, VariationAdaptor and PopulationAdaptor, to use vcf(1) when I want both database and vcf data? I mainly use it to get out variants in LD with each other.
Will setting different vcfs on the different adaptors affect the variants extracted? Or is it enough to set vcf(1) on the VariationAdaptor, for instance?</div>
<div class=""><br class="">
</div>
<div class="">Even though the super populations are not on the printed list when using the population adaptor to print out all LD populations, is it possible to use $population_adaptor->fetch_by_name(‘EUR’) for instance? I tried this, but got no variants in
LD. Do you have any ways this is possible to do, or a alternative list of super populations one can generate in some way? Or should I simply gather all subpopulations, such as EUR = (CEU, TSI, FIN, GBR, IBS) and loop through all these to get the super population
LD?</div>
<div class=""><br class="">
</div>
<div class="">Here is a script where I tried to use the super population «EUR» directly, without success (but no error message either, it just finds no LD variants):</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""><font face="Courier New" class="">use strict;</font></div>
<div class=""><font face="Courier New" class="">use warnings;</font></div>
<div class=""><font face="Courier New" class="">use Bio::EnsEMBL::Registry;</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">my $inputfile = $ARGV[0];</font></div>
<div class=""><font face="Courier New" class="">my $outputfile = $ARGV[1];</font></div>
<div class=""><font face="Courier New" class="">my $r_limit = $ARGV[2];</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">open (IN, "<$inputfile");</font></div>
<div class=""><font face="Courier New" class="">open (OUT, ">$outputfile");</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">my $registry = 'Bio::EnsEMBL::Registry';</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">$registry->load_registry_from_db(</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>-host => '<a href="http://ensembldb.ensembl.org/" class="">ensembldb.ensembl.org</a>',</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>-user => 'anonymous'</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>);</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""># Connect to the databases:</font></div>
<div class=""><font face="Courier New" class="">my $variation_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'variation');</font></div>
<div class=""><font face="Courier New" class="">my $ldfc_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'ldfeaturecontainer');</font></div>
<div class=""><font face="Courier New" class="">my $pop_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'population');</font></div>
<div class=""><font face="Courier New" class="">$variation_adaptor->db->use_vcf(1);</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">my $ld_population = $pop_adaptor->fetch_by_name('EUR');</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""># Loop through all SNPs available and find SNPs in LD</font></div>
<div class=""><font face="Courier New" class="">while(<IN>) {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>chomp;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $variation_name = $_;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $variation = $variation_adaptor->fetch_by_name($variation_name);</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my @var_features = @{ $variation->get_all_VariationFeatures() };</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>foreach my $vf (@var_features) {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $rsid = $vf->name;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>print $rsid, "\n";</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $start = $vf->start;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $region = $vf->seq_region_name;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>print OUT "$region\t$rsid\t$start\n";</font></div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"><font face="Courier New" class=""></font></span></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $ldfc = $ldfc_adaptor->fetch_by_VariationFeature($vf, $ld_population);</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my @ld_values = @{ $ldfc->get_all_ld_values() };</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>foreach my $ld_hash (@ld_values) {</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>my $r2 = $ld_hash->{r2};</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>
<span class="Apple-tab-span" style="white-space:pre"></span>if ($r2 >= $r_limit) {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $variation_name1 = $ld_hash->{variation1}->variation_name;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $variation_name2 = $ld_hash->{variation2}->variation_name;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $pos1 = $ld_hash->{variation1}->seq_region_name;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $pos2 = $ld_hash->{variation2}->seq_region_name;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $start1 = $ld_hash->{variation1}->start;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $start2 = $ld_hash->{variation2}->start;</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>if ($variation_name1 eq $rsid) {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>print OUT "$pos2\t$variation_name2\t$start2\tr2=$r2\n";</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>} else {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>print OUT "$pos1\t$variation_name1\t$start1\tr2=$r2\n"; <span class="Apple-tab-span" style="white-space:pre">
</span></font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>}</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>}</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>}</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</font></div>
<div class=""><font face="Courier New" class="">}</font></div>
<div class=""><font face="Courier New" class="">close OUT;</font></div>
<div class=""><font face="Courier New" class="">close IN;</font></div>
</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Johanne Håøy Horn</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
</div>
</div>
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