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  1. Barna Package
  2. BARNA-388

Allow reading of (b)gzip-compressed VCF files

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    Details

    • Type: Improvement
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: AStalavista 3.2 (API 1.22)
    • Fix Version/s: None
    • Component/s: Astalavista
    • Labels:
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      Description

      Astalavista can read gzip-compressed GTF files, but not (b)gzip-compressed VCF files. (Note that bgzip-compressed files are compatible with normal gzip files.)

      Given that nowadays it is common for variant data to be provided as (tabix-indexed) bgzipped VCF files, and given the large sizes of genomic scale variant files, it would be convenient if Astalavista could read them directly rather than requiring them to be decompressed.

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            Assignee:
            micha Micha Sammeth
            Reporter:
            martin Martin Oti
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              Dates

              Created:
              Updated: