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./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz
./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz
--info TestDataImputedVCF.info
--info TestDataImputedVCF.info (NOT mandatory)
--prefix OutPrefix
--prefix OutPrefix
--type plink
--type plink
--format 1
--format 1
This command line would create three files : <code> OutPrefix.plink.dosage.gz, OutPrefix.fam, OutPrefix.map </code>
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).
== Convert to MaCH Files ==
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].
./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz
--info TestDataImputedVCF.info (NOT mandatory)
--prefix OutPrefix
--type plink
--format 1
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).
The command options for DosageConvertor are explained below.
The command options for DosageConvertor are explained below.
