[ensembl-dev] Variation (VEP) 2.5 - Het/Hom Output - Plugin Attached

[Ricardo Parolin Schnekenberg]

Following on the thread 2012-May/007541.html and with the kind help of
Will McLaren, I came up with a little plugin that outputs a HomHet=HOM or
HomHet=HET in the Extra column of the VEP output (as long as you are using
the --individual flag).

It relies on the VEP.pm detecting that the --individual flag is turned on
and then parsing the extra column, splitting on the /:/ and getting the
first element [0], which carries the genotype of each individual in a 0/0
1/1 0/1 0/1 form (And it considers the possibility of being a forward
slash, backslash or pipe). Then it saves it as the allele_string of
variation_feature.

The plugin itself just grabs whatever data is in allele_string and splits
the slashes/pipes and counts the number of "alleles".

>2 alleles (eg: A/C/C) means homozygous (check line 518 of VEP.pm)
<=2 alleles (e.g A/C) means heterozygous.

I don't think VEP would output a line if there was no variant (so
allele_string would be just $ref), but in that case change it accordingly.

I am a medic, not a programmer so please check/recheck the code. It might
be just totally wrong, which would be embarassing, but oh well.


############
## HOM/HET Plugin
## To be used with VEP 2.5 Onwards (which support the --individual option)
## By Ricardo Parolin Schnekenberg
## Wellcome Trust Centre for Human Genetics / University of Oxford

package HomHet;

use strict;
use warnings;

use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
use Bio::EnsEMBL::Variation::Utils::VEP;

use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);

sub new {
    my $class = shift;

    my $self = $class->SUPER::new(@_);

    die "ERROR: You must be using --individual to use this plugin\n"
unless defined($self->{config}->{individual});

    return $self;
}

sub version {
    return '2.5';
}

sub feature_types {
    return ['Feature','Intergenic'];
}

sub get_header_info {
    return {
        HomHet => "Zygosity of individual genotype",
    };
}

sub run {
    my ($self, $tva) = @_;

    my $tv = $tva->transcript_variation;
    my $vf = $tv->variation_feature;


    my $allele_string = $vf->{allele_string};
    return {} unless defined $allele_string;

        my @alleles = split /\||\/|\\/, $allele_string;


    my $hom_het = scalar @alleles > 2 ? 'HOM' : 'HET';





return {
        HomHet => $hom_het,
    }
}

1;


-- 
Ricardo Parolin Schnekenberg
Genomics Research
Wellcome Trust Centre for Human Genetics
University of Oxford