[ensembl-dev] unable to recover high-r2 pair using fetch_by_VariationFeatures

[andrew126 at mac.com]

Hi,

I am using API version 86.

There are two snps within 1kb of each other that have a high r2 value:

rs79796976 (chr1, pos 247,390,677)
rs56285508 (chr1, pos 247,391,186)
r^2 0.983802 in 1000GENOMES:phase_3:EUR

I can recover rs56285508 as a high-LD pair when I use fetch_by_VariationFeature (no “s” at the end), querying with rs79796976.

However, I get no result when I use fetch_by_VariationFeatures (with an “s” at the end), querying with both snps.

Below is the perl script using fetch_by_VariationFeatures.

Can you please let me know if I am using fetch_by_VarationFeatures incorrectly?

Thanks for any guidance.

Best regards,

Andrew



use strict;
$|=1;
use IPC::Run;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::ApiVersion; 
printf( "The API version used is %s\n", software_version() ); 

my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_all();
$registry->set_reconnect_when_lost(1);
$registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org', # alternatively ensembldb 'useastdb.ensembl.org'
    -user => 'anonymous'
    );

my $chrom = "1";
my $var1 = "rs79796976";
my $region_start1 = "247390677";
my $region_end1 = "247390677";
my $var2 = "rs56285508";
my $region_start2 = "247391186";
my $region_end2 = "247391186";

my $pop_adaptor = $registry->get_adaptor("human","variation","population");
$pop_adaptor->db->use_vcf(1);
my $ldFeatureContainerAdaptor = $registry->get_adaptor('human', 'variation', 'ldfeaturecontainer');
$ldFeatureContainerAdaptor->db->use_vcf(1);
my $variation_adaptor = $registry->get_adaptor( 'human', 'variation', 'variation' );
$variation_adaptor->db->use_vcf(1);
	
my $population_name = "1000GENOMES:phase_3:EUR";
my $population = $pop_adaptor->fetch_by_name($population_name);
	
my $variation1 = $variation_adaptor->fetch_by_name("$var1");
my $vfref1 = $variation1->get_all_VariationFeatures();
my $query_variation_feature1;
my $found=0;
foreach my $vf1 (@{$vfref1}) {
    if ($chrom eq $vf1->seq_region_name) {
	if ($region_start1 eq $vf1->seq_region_start && $region_end1 eq $vf1->seq_region_end) {
	    $found=1;
	    $query_variation_feature1 = $vf1;
	}
    }
}
if ($found==0) {die;}

my $variation2 = $variation_adaptor->fetch_by_name("$var2");
my $vfref2 = $variation2->get_all_VariationFeatures();
my $query_variation_feature2;
$found=0;
foreach my $vf2 (@{$vfref2}) {
    if ($chrom eq $vf2->seq_region_name) {
	if ($region_start2 eq $vf2->seq_region_start && $region_end2 eq $vf2->seq_region_end) {
	    $found=1;
	    $query_variation_feature2 = $vf2;
	}
    }
}
if ($found==0) {die;}

my $ldFeatureContainer = $ldFeatureContainerAdaptor->fetch_by_VariationFeatures([$query_variation_feature1, $query_variation_feature2],$population);

foreach my $r_square (@{$ldFeatureContainer->get_all_r_square_values}){
    if ($r_square->{r2} >= 0.1){ 
	print $r_square->{variation1}->variation_name."\n";
	print "\t".$r_square->{variation1}->seq_region_start."\n";
	print "\t".$r_square->{variation1}->seq_region_end."\n";
	print $r_square->{variation2}->variation_name."\n";
	print "\t".$r_square->{variation2}->seq_region_start."\n";
	print "\t".$r_square->{variation2}->seq_region_end."\n";
	print "r^2 ".$r_square->{r2}."\n";
    }
}