Changes

  make

  make

The command options for DosageConvertor are explained below. <code>"vcfDose"</code> is a mandatory parameter requiring the input VCF file. <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>"--prefix"</code> denotes the output file prefix (default value: <code>Converted.Dosage</code>). <code>"--type"</code> denotes the output file format (available options: <code>mach</code> (default) and <code>plink</code>). <code>"--format"</code> decides whether to import imputed values from dosage (<code>DS</code>, default) or genotype probabilities (<code>GP</code>) of the input VCF file. <code>"--buffer"</code> denotes the number of markers to import at a time (valid only for MaCH format). <code>"--idDelimiter  "</code> denotes the delimiter to Split VCF Sample ID into FID and IID for PLINK format

The command options for DosageConvertor are explained below.  

 

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

 

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

<code>""</code>

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