Difference between revisions of "DosageConvertor"
From Genome Analysis Wiki
Jump to navigationJump to searchSanty.8128 (talk | contribs) |
Santy.8128 (talk | contribs) |
||
| Line 34: | Line 34: | ||
make | make | ||
| − | |||
| − | Usage: ./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz | + | Usage: ./DosageConvertor --vcfDose TestDataImputedVCF.dose.vcf.gz |
--info TestDataImputedVCF.info | --info TestDataImputedVCF.info | ||
--prefix OutputFilePrefix | --prefix OutputFilePrefix | ||
| Line 47: | Line 46: | ||
--idDelimiter _ // Delimiter to Split VCF Sample ID into | --idDelimiter _ // Delimiter to Split VCF Sample ID into | ||
// FID and IID for PLINK format | // FID and IID for PLINK format | ||
| − | + | ||
Revision as of 19:17, 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
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.
