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  1. UGENE
  2. UGENE-4567

Integrate PLINK for whole genome association analysis

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Minor
    • Resolution: Won't Fix
    • Affects Version/s: 1.17
    • Fix Version/s: None
    • Component/s: NGS
    • Affect Type:
      Userdefined

      Description

      PLINK homepage: http://pngu.mgh.harvard.edu/~purcell/plink/

      Consider to embed the following workflow as well:

      1. Variant Calling (with SAMtools or Pilon - see UGENE-4566)
      2. VCF file filtration - using vcftools and maybe additional scripts
      3. Convertion to formats, required by PLINK (fam, bed, bim)
      4. Producing of GWAS reports by PLINK

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          Issue Links

          relates to

          New Feature - A new feature of the product, which has yet to be developed. UGENE-4566 Integrate Pilon for variant calling

          • Trivial - Cosmetic problem like misspelt words or misaligned text.
          • Closed

            Activity

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              Assignee:
              Unassigned
              Reporter:
              oigl Olga Golosova
              Watchers:
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                Dates

                Created:
                Updated:
                Resolved: