DosageConvertor: Difference between revisions
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= Introduction = | = Introduction = | ||
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK. | DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK. | ||
= Download = | = Download = | ||
'''VERSION: 1.0. | '''VERSION: 1.0.2 !!! (Updated 6.6.2016) !!!''' | ||
'''Github Repo:''' Users can clone from github repository as well : [https://github.com/Santy-8128/ | '''Github Repo:''' Users can clone from github repository as well : [https://github.com/Santy-8128/DosageConvertor Github] | ||
'''Cloning from GitHub is recommened so that updates can be easily pulled back !!!''' | '''Cloning from GitHub is recommened so that updates can be easily pulled back !!!''' | ||
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! Download Link | ! Download Link | ||
|- | |- | ||
| | | DosageConvertor Source Files | ||
| [ftp://share.sph.umich.edu/ | | | ||
[ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertor.v1.0.2.tar.gz UNIX Users ] | |||
|} | |} | ||
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= Usage= | = Usage= | ||
Users should follow the following steps to compile ''' | Users should follow the following steps to compile '''DosageConvertor ''' (if they downloaded the source files). | ||
## EXTRACT M3VCFTOOLS AND COMPILE | ## EXTRACT M3VCFTOOLS AND COMPILE | ||
| | ||
tar -xzvf | tar -xzvf DosageConvertor.v1.0.2.tar.gz | ||
cd | cd DosageConvertor/ | ||
make | make | ||
For e.g. to calculate LD the command should be: <code>. | For e.g. to calculate LD the command should be: <code> | ||
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 | |||
</code> | |||
= Contact = | = Contact = | ||
In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das]. | In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das]. | ||
Revision as of 19:11, 6 June 2016
- 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: 1.0.2 !!! (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 |
Usage
Users should follow the following steps to compile DosageConvertor (if they downloaded the source files).
## EXTRACT M3VCFTOOLS AND COMPILE tar -xzvf DosageConvertor.v1.0.2.tar.gz cd DosageConvertor/ make
For e.g. to calculate LD the command should be:
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.
