Details
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Type: Bug
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Status: Closed
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Priority: Major
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 2.11.0
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Component/s: None
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Labels:
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Epic Link:
Description
A corner case when processing VCF variants to a reverse strand sequence.
Example: BRAF is ENSG00000157764 GRCh38:7:140719327:140924764:-1
Insertion G,GTATT at position 140924424 of genomic sequence
G maps to (complement) C at position 341 of transcript ENST288602, position 280 of CDS.
genomic (forward strand): G (insertion) TATT T
could be shown as
gene/transcript (reverse strand complement): A (insertion) AATA C
i.e. a reverse complement insertion on the _preceding_ position?
Currently Jalview renders as C,AATAC which makes no sense (start base of insertion should match reference base).
Example: BRAF is ENSG00000157764 GRCh38:7:140719327:140924764:-1
Insertion G,GTATT at position 140924424 of genomic sequence
G maps to (complement) C at position 341 of transcript ENST288602, position 280 of CDS.
genomic (forward strand): G (insertion) TATT T
could be shown as
gene/transcript (reverse strand complement): A (insertion) AATA C
i.e. a reverse complement insertion on the _preceding_ position?
Currently Jalview renders as C,AATAC which makes no sense (start base of insertion should match reference base).
Attachments
Issue Links
- related with
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JAL-2738 Support loading VCF on to human gene sequence
- Closed