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-Victor Sample matching and validate tools

3.0. Files:

  • MAKE SURE THAT BLUP/BLUEs ARE CALCULATED FROM: Phenotype.TSV- need to replace this phenotype file with BLUP/BLUE output


3.1. Choose "Genotype-Phenotype Matching genotype and phenotype files" from the "Genomic Selection Tools."

    3.1.1. In the "Encoded Genotype Data," choose "Genotype.HMP"

    3.1.2. In the "Phenotype Data," choose "BLUP output data"

    3.1.3. For "Column Header for GID in the Phenotype File," choose "c1: gid"

    3.1.4. For "Grouping Factor", click on "Insert Grouping Factor" and choose "c2: Environment" for "Column Hearder for a Grouping Factor in the Phenotype File."

    3.1.5. Input "2", in the "Row Start Number for the Observations in the Phenotype File"

    3.1.6. Click "Execute"

3.2. The result will be two files:

    3.2.1. Sample Matching Output (tab delimitted file that contains both training and prediction set for Genomic Selection)

    3.2.2. Genotype Matrix Output (this is no longer in hapmap but a generic matrix, with rows as markers and columns as samples/lines)

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