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, 17:58, 11 July 2017
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| | == Converting Chromosome X Files == | | == Converting Chromosome X Files == |
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| − | The following command line should convert a input VCF dosage file to a MaCH/minimac dosage file (the format that available in the earlier version of [Minimac minimac]). The generated dosage files can be tested for association using [http://genome.sph.umich.edu/wiki/Mach2dat:_Association_with_MACH_output mach2dat].
| + | No extra parameter is necessary for converting chromosome X files. |
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| − | ./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz
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| − | --info TestDataImputedVCF.info (NOT mandatory)
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| − | --prefix OutPrefix
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| − | --type plink
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| − | --format 1
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| − | This command line would create three files : <code> OutPrefix.plink.dosage.gz, OutPrefix.fam, OutPrefix.map </code>. The <code>--format</code> parameter can take values 1, 2 and 3. Each of these values correspond to the three different formats available for PLINK dosage files (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 needs to be manually edited before PLINK can run association testing).
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| | + | ** |
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| | = Command Line Options = | | = Command Line Options = |
