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Dear Ensembl team,
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<div class="">Thank you for previous help with setting up the API!</div>
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<div class="">I am now able to use the API properly using the scripts of the tutorial pages of LD available from the ensembl blog and web page.</div>
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<div class="">What I now try to do, is to expand a list of tag/index SNPs from GWAS to include the SNPs in LD with the input SNPs. The code I have is the following:</div>
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<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>
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<div class=""><font face="Courier New" class="">my $registry = 'Bio::EnsEMBL::Registry';</font></div>
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</font></div>
<div class=""><font face="Courier New" class="">$registry->load_registry_from_db(</font></div>
<div class=""><font face="Courier New" class=""> -host => '<a href="http://ensembldb.ensembl.org" class="">ensembldb.ensembl.org</a>',</font></div>
<div class=""><font face="Courier New" class=""> -user => 'anonymous'</font></div>
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</font></div>
<div class=""><font face="Courier New" class="">my $variation_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'variation' );</font></div>
<div class=""><font face="Courier New" class="">$variation_adaptor->db->use_vcf(1); # To get 1000G phase 3 data also</font></div>
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</font></div>
<div class=""><font face="Courier New" class="">while (<>) {</font></div>
<div class=""><font face="Courier New" class=""> chomp; # Remove \n from input file line names</font></div>
<div class=""><font face="Courier New" class=""> my $variation = $variation_adaptor->fetch_by_name($_);</font></div>
<div class=""><font face="Courier New" class=""> print $variation->stable_id(), "\n";</font></div>
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</font></div>
<div class=""><font face="Courier New" class=""> my @vfs = @{ $variation->get_all_VariationFeatures() };</font></div>
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<div class=""><font face="Courier New" class=""> foreach my $vf (@vfs){</font></div>
<div class=""><font face="Courier New" class=""> print "get ld values\n";</font></div>
<div class=""><font face="Courier New" class=""> my $ld = $vf->get_all_LD_values();</font></div>
<div class=""><font face="Courier New" class=""> print "get ld variations\n";</font></div>
<div class=""><font face="Courier New" class=""> my @ldvs = @{ $ld->get_variations() };</font></div>
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</font></div>
<div class=""><font face="Courier New" class=""> print "for each ld variation\n";</font></div>
<div class=""><font face="Courier New" class=""> foreach my $ldv (@ldvs) {</font></div>
<div class=""><font face="Courier New" class=""> print $ldv->stable_id();</font></div>
<div class=""><font face="Courier New" class=""> }</font></div>
<div class=""><font face="Courier New" class=""> } </font></div>
<div class=""><font face="Courier New" class="">}</font></div>
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<div class="">When calling $vf->get_all_LD_values I get the following error/warning:</div>
<div class=""><font face="Courier New" class="">Use of uninitialized value $gt[1] in hash element at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/LDFeatureContainerAdaptor.pm line 716.</font></div>
<div class=""><font face="Courier New" class="">...</font></div>
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<div class=""><font face="Courier New" class="">Use of uninitialized value in string ne at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/LDFeatureContainerAdaptor.pm line 617.</font></div>
<div class=""><font face="Courier New" class="">...</font></div>
<div class=""><font face="Courier New" class="">Number of genotypes supported by the program (500) exceeded</font></div>
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<div class=""><font face="Courier New" class="">...</font></div>
<div class=""><font face="Courier New" class="">Can't call method "get_all_VariationFeatures" on an undefined value at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/LDFeatureContainerAdaptor.pm line 870, <OUT> line 29120.</font></div>
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<div class="">The «…» means the warning/error is printed multiple times in a row.</div>
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<div class="">I have described the issue in further detail here: <a href="https://www.biostars.org/p/178467/" class="">https://www.biostars.org/p/178467/</a></div>
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<div class="">Could you help me with what I am doing wrong? Also, is there a better way of finding all SNPs in LD with an input SNP than the one I am trying to do? Speed seems to be an issue when the number of SNPs get large.</div>
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<div class="">Best</div>
<div class="">Johanne Håøy Horn</div>
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