DosageConvertor

• Download Pilot Version 1.0.1 !!! (Updated June 2015) !!!

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
DosageConvertor Source Files	UNIX Users

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.