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Web VEP: fix incorrect variant end #1059

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Web VEP: fix incorrect variant end #1059

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fe6aab1
Fix incorrect variant end in web VEP
nuno-agostinho Nov 30, 2023
da68ff6
Fix unit tests
nuno-agostinho Dec 1, 2023
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6 changes: 4 additions & 2 deletions modules/Bio/EnsEMBL/Variation/VariationFeature.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -2340,6 +2340,8 @@ sub to_VCF_record {
$non_acgt = 1 if $allele && $allele !~ /^[ACGTN\.]+$/;
}

my $INFO = $self->end ? 'END='.$self->end : '.';

# in/del/unbalanced
if($non_acgt || scalar keys %allele_lengths > 1) {

Expand Down Expand Up @@ -2382,7 +2384,7 @@ sub to_VCF_record {
$self->variation_name || '.',
shift @alleles,
(join ",", @alleles) || '.',
'.', '.', '.'
'.', '.', $INFO
];

}
Expand All @@ -2395,7 +2397,7 @@ sub to_VCF_record {
$self->variation_name || '.',
shift @alleles,
(join ",", @alleles) || '.',
'.', '.', '.'
'.', '.', $INFO
];
}
}
Expand Down
24 changes: 12 additions & 12 deletions modules/t/variationFeature.t
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Original file line number Diff line number Diff line change
Expand Up @@ -161,50 +161,50 @@ my $sr_start = $vf->seq_region_start;

is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start, $vname, 'A', 'T', '.', '.', '.'],
[$chr, $sr_start, $vname, 'A', 'T', '.', '.', "END=$end"],
'to_VCF_record'
);

$vf->strand(-1);
is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start, $vname, 'T', 'A', '.', '.', '.'],
[$chr, $sr_start, $vname, 'T', 'A', '.', '.', "END=$end"],
'to_VCF_record - rev strand'
);
$vf->strand($strand);

$vf->allele_string('A/G/T');
is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start, $vname, 'A', 'G,T', '.', '.', '.'],
[$chr, $sr_start, $vname, 'A', 'G,T', '.', '.', "END=$end"],
'to_VCF_record - multiple alts'
);

$vf->allele_string('AG/CT');
is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start, $vname, 'AG', 'CT', '.', '.', '.'],
[$chr, $sr_start, $vname, 'AG', 'CT', '.', '.', "END=$end"],
'to_VCF_record - balanced non-SNP'
);

$vf->allele_string('A/-');
is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start - 1, $vname, 'NA', 'N', '.', '.', '.'],
[$chr, $sr_start - 1, $vname, 'NA', 'N', '.', '.', "END=$end"],
'to_VCF_record - deletion'
);

$vf->allele_string('-/A');
is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start - 1, $vname, 'N', 'NA', '.', '.', '.'],
[$chr, $sr_start - 1, $vname, 'N', 'NA', '.', '.', "END=$end"],
'to_VCF_record - insertion'
);

$vf->allele_string('A/-/G');
is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start - 1, $vname, 'NA', 'N,NG', '.', '.', '.'],
[$chr, $sr_start - 1, $vname, 'NA', 'N,NG', '.', '.', "END=$end"],
'to_VCF_record - mixed'
);

Expand All @@ -213,21 +213,21 @@ $vf->allele_string('HGMD_MUTATION');
$vf->{class_SO_term} = 'SNV';
is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start, $vname, 'N', 'N', '.', '.', '.'],
[$chr, $sr_start, $vname, 'N', 'N', '.', '.', "END=$end"],
'to_VCF_record - unknown alleles SNV'
);

$vf->{class_SO_term} = 'insertion';
is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start - 1, $vname, 'N', '<INS>', '.', '.', '.'],
[$chr, $sr_start - 1, $vname, 'N', '<INS>', '.', '.', "END=$end"],
'to_VCF_record - unknown alleles insertion'
);

$vf->{class_SO_term} = 'deletion';
is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start - 1, $vname, 'NN', 'N', '.', '.', '.'],
[$chr, $sr_start - 1, $vname, 'NN', 'N', '.', '.', "END=$end"],
'to_VCF_record - unknown alleles deletion'
);

Expand All @@ -242,14 +242,14 @@ my $fully_justified_allele_str = 'ACGTGGACG/ACG/ACGTGGACGTGGACG';
$vf->allele_string($fully_justified_allele_str);
is_deeply(
$vf->to_VCF_record(),
[$chr, $sr_start, $vname, 'ACGTGGA', 'A,ACGTGGACGTGGA', '.', '.', '.'],
[$chr, $sr_start, $vname, 'ACGTGGA', 'A,ACGTGGACGTGGA', '.', '.', "END=$end"],
'to_VCF_record - fully justified allele string clipped'
);


is_deeply(
$vf->to_VCF_record(1),
[$chr, $sr_start, $vname, 'ACGTGGACG', 'ACG,ACGTGGACGTGGACG', '.', '.', '.'],
[$chr, $sr_start, $vname, 'ACGTGGACG', 'ACG,ACGTGGACGTGGACG', '.', '.', "END=$end"],
'to_VCF_record - fully justified allele string not clipped'
);

Expand Down