Changes

== Convert to PLINK Files ==

== Convert to PLINK Files ==

The following command line should convert a input VCF dosage file to a PLINK dosage file that can be tested for association in PLINK1.07, PLINK1.9, PLINK2.0.  

The following command line should convert a input VCF dosage file to a PLINK dosage file that can be tested for association in [https://www.cog-genomics.org/plink2 PLINK1.9] or [https://www.cog-genomics.org/plink/2.0/ PLINK2.0].  

  ./DosageConvertor        --vcfDose      TestDataImputedVCF.dose.vcf.gz

  ./DosageConvertor        --vcfDose      TestDataImputedVCF.dose.vcf.gz

                           --info        TestDataImputedVCF.info (NOT mandatory)

                           --info        TestDataImputedVCF.info         (NOT mandatory)

                           --prefix      OutPrefix

                           --prefix      OutPrefix

                           --type        plink

                           --type        plink                           (default)

                           --format      1

                           --format      1                               (or 2,3)

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).

This command line would create three files :  <code> OutPrefix.plink.dosage.gz, OutPrefix.fam, OutPrefix.map</code>. The <code>.fam</code> and <code>.map</code> formats have been described [http://zzz.bwh.harvard.edu/plink/data.shtml#map here]. 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 <code>OutPrefix.fam</code> does NOT contain sex information unless chromosome X is available. See [[#Converting Chromosome X Files]] for more details.

== Convert to MaCH Files ==

== Convert to MaCH Files ==