Difference between revisions of "DosageConvertor"
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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. | ||
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= 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> | ||
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= 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.
