DosageConvertor

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  • Download Release Version 1.0.3 !!! (Updated June 2016) !!!

Introduction

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK.

Download

VERSION: 1.0.3 !!! (Updated 6.6.2016) !!!

Github Repo: Users can clone from github repository as well : Github

Cloning from GitHub is recommened so that updates can be easily pulled back !!!

Description Download Link
Source Files

UNIX Users

Binary Executable

UNIX Users

Binary executables are NOT guaranteed to run on every LINUX machine. Please compile from source file if you have trouble with the executable, or else contact the author Sayantan Das..

Usage

Users should follow the following steps to compile DosageConvertor (if they downloaded the source files).

## EXTRACT M3VCFTOOLS AND COMPILE
 
wget ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertor.v1.0.3.tar.gz
tar -xzvf DosageConvertor.v1.0.3.tar.gz
cd DosageConvertor/
make

The command options for DosageConvertor are explained below.

  • "--vcfDose" is a mandatory parameter requiring the input VCF file.
  • "--info" 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.
  • "--prefix" denotes the output file prefix (default value: Converted.Dosage).
  • "--type" denotes the output file format (available handles: mach (default) and plink).
  • "--format" decides whether to import imputed values from dosage (DS) or genotype probabilities (GP) of the input VCF file (available handles: DS (default) and GP).
  • "--buffer" denotes the number of markers to import at a time (valid only for MaCH format) (default value 10000).
  • "--idDelimiter " denotes the delimiter to Split VCF Sample ID into FID and IID for PLINK format (default value _).
Usage: ./DosageConvertor  --vcfDose      TestDataImputedVCF.dose.vcf.gz
                          --info         TestDataImputedVCF.info
                          --prefix       OutputFilePrefix
                          --type         plink OR mach   // depending on output format
                          --format       DS or GP        // based on if you want to output
                                                         // dosage (DS) or genotype prob (GP)
                          --buffer       10000           // Number of Markers to import and
                                                         // print at a time (valid only for
                                                         // MaCH format)
                          --idDelimiter  _               // Delimiter to Split VCF Sample ID into
                                                         // FID and IID for PLINK format

Contact

In case of any queries and bugs please contact Sayantan Das.