Difference between revisions of "DosageConvertor"
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[ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertor.v1.0.3.tar.gz UNIX Users ] | [ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertor.v1.0.3.tar.gz UNIX Users ] | ||
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| − | | Binary Executable | + | | Binary Executable <sup>†</sup> |
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[ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertorExecutable.tar.gz UNIX Users ] | [ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertorExecutable.tar.gz UNIX Users ] | ||
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| − | '''<sup> | + | '''<sup>†</sup>''' 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 [mailto:sayantan@umich.edu Sayantan Das].. |
= Usage= | = Usage= | ||
Revision as of 18:37, 7 June 2016
- 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 | |
| Binary Executable † |
† 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
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.
