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, 19:48, 11 July 2017
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| --format 1 (or 2,3) | | --format 1 (or 2,3) |
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− | This command will create three files : <code> OutPrefix.plink.dosage.gz, OutPrefix.fam, OutPrefix.map</code>. The <code>.fam</code> and <code>.map</code> formats are described [http://zzz.bwh.harvard.edu/plink/data.shtml#map here]. The <code>--format</code> parameter can take values 1, 2, or 3. Each of these values correspond to the three different PLINK dosage file formats (details on PLINK dosage files are given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here]). Note that the generated <code>OutPrefix.map</code> does NOT contain any phenotype information (which will need to be manually edited before PLINK can perform association tests). The <code>OutPrefix.fam</code> will NOT contain sex information unless chromosome X is available. See [[#Converting Chromosome X Files | Converting Chromosome X Files]] for details. | + | This command will create three files : <code>OutPrefix.plink.dosage.gz</code>, <code>OutPrefix.fam</code>, and <code>OutPrefix.map</code>. The <code>.fam</code> and <code>.map</code> formats are described [http://zzz.bwh.harvard.edu/plink/data.shtml#map here]. The <code>--format</code> parameter can take values 1, 2, or 3. Each of these values correspond to the three different PLINK dosage file formats (details on PLINK dosage files are given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here]). Note that the generated <code>OutPrefix.map</code> does NOT contain any phenotype information (which will need to be manually edited before PLINK can perform association tests). The <code>OutPrefix.fam</code> will NOT contain sex information unless chromosome X is available. See [[#Converting Chromosome X Files | Converting Chromosome X Files]] for details. |
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| == Convert to MaCH Files == | | == Convert to MaCH Files == |