Details
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Type: Bug
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Status: Closed
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Priority: Major
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Resolution: Not A Bug
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Affects Version/s: 2.10.0
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Fix Version/s: 2.10.0
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Component/s: data retrieval services
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Labels:None
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Epic Link:
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Urgency:Urgent
Description
The Ensembl variant view, for human at least, ought to faithfully preserve the 'clinical_significance' annotation for variants observed in a locus. Although the annotation appears to be present when exporting variant data from Jalview, its value is 'ARRAY(..)' - suggesting something along the data-retrieval chain is broken.
1. select the Ensembl sequence source and import the example gene accession
2. Export the features as GFF to text box. Variant features include something like:
ENST00000479537 . sequence_variant 734 734 0.0 + . ID=sequence_variant:rs373128505;alleles=A,G;assembly_name=GRCh38;clinical_significance=ARRAY(0xf095520);consequence_type=3_prime_UTR_variant
The ARRAY(0x...) looks like a server issue (raw array reference in perl?), but should be investigated.
1. select the Ensembl sequence source and import the example gene accession
2. Export the features as GFF to text box. Variant features include something like:
ENST00000479537 . sequence_variant 734 734 0.0 + . ID=sequence_variant:rs373128505;alleles=A,G;assembly_name=GRCh38;clinical_significance=ARRAY(0xf095520);consequence_type=3_prime_UTR_variant
The ARRAY(0x...) looks like a server issue (raw array reference in perl?), but should be investigated.