DosageConvertor

• 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 ExecutableTemplate:Dagger *	UNIX Users

^* Before running downloaded binary file run chmod +x DosageConvertor

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

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.