Changes

The command options for DosageConvertor are explained below.  

The command options for DosageConvertor are explained below.  

*<code>"--vcfDose"</code> is a mandatory parameter requiring the input VCF dosage file from minimac3/4.  

*<code>--vcfDose</code> is a mandatory parameter requiring the input VCF dosage file from minimac3/4.  

*<code>"--info"</code> denotes the info file from the same imputation output. This parameter is NOT mandatory, but if NO info file is provided, the output MaCH info file will have some missing columns.  

*<code>--info</code> denotes the info file from the same imputation output. This parameter is optional, but if NO info file is provided, the output MaCH info file will have some missing columns.  

*<code>"--prefix"</code> denotes the output file prefix (default value: <code>Converted.Dosage</code>).  

*<code>--prefix</code> denotes the output file prefix (default value: <code>Converted.Dosage</code>).  

*<code>"--type"</code> denotes the output file format (available handles: <code>mach</code> (default) and <code>plink</code>).  

*<code>--type</code> denotes the output file format (available handles: <code>plink</code> (default) and <code>mach</code>).  

*<code>"--format"</code> decides whether to import imputed values from dosage (<code>DS</code>) or genotype probabilities (<code>GP</code>) of the input VCF file (available handles: <code>DS</code> (default) and <code>GP</code>).  

*<code>--tag</code> decides whether to import imputed values from dosage (<code>DS</code>: default), or genotype probabilities (<code>GP</code>), or hard call genotypes (<code>GT</code>) of the input VCF file.

*<code>"--buffer"</code> denotes the number of markers to import at a time (valid only for MaCH format) (default value <code>10000</code>).  

*<code>--format</code> decides the format of the output file. If <code>--type mach</code> is used, <code>--format</code> can take values 1, 2 and 3. Each of these values correspond to the three different formats available for PLINK dosage files (details given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here]). If <code>--type mach</code> is used, <code>--format</code> can only take values 1 and 2. Details are given in [[#Convert to MaCH Files]]

*<code>"--idDelimiter "</code> denotes the delimiter to Split VCF Sample ID into FID and IID for PLINK format (default value <code>_</code>).

 

*<code>--buffer</code> denotes the number of markers to import at a time (valid only for MaCH format) (default value <code>10000</code>).  

*<code>--idDelimiter</code> denotes the delimiter to Split VCF Sample ID into FID and IID for PLINK format (default value <code>_</code>).

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

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