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  1. Jalview
  2. JAL-2738

Support loading VCF on to human gene sequence

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.11.0
    • Component/s: cds/protein
    • Labels:
      None

      Description

      Add the ability to read VCF data (plain or compressed/indexed) and add to a human gene sequence in Jalview as variant features. Also add to derived transcripts, and compute and add as peptide variants on any protein product sequences.

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          depends on

          New Feature - A new feature of the product, which has yet to be developed. JAL-1796 process ensembl style genome coordinates in FASTA description lines

          • Major - Major loss of function.
          • In Progress
          related with

          New Feature - A new feature of the product, which has yet to be developed. JAL-2743 Support loading VCF to non-human sequences

          • Major - Major loss of function.
          • In Progress

          Bug - A problem which impairs or prevents the functions of the product. JAL-2845 Correct processing of reverse strand VCF insertion alleles

          • Major - Major loss of function.
          • Closed

          New Feature - A new feature of the product, which has yet to be developed. JAL-2755 Load VCF to CDS cross-ref from protein

          • Critical - Crashes, loss of data, severe memory leak.
          • Ready for testing

          Improvement - An improvement or enhancement to an existing feature or task. JAL-3469 Read ClinVar VCF data

          • Major - Major loss of function.
          • Ready for testing

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Dates

                Created:
                Updated:
                Resolved: