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  1. Jalview
  2. JAL-2845

Correct processing of reverse strand VCF insertion alleles

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.11.0
    • Component/s: None
    • Labels:

      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).

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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