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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: 1.0.1 !!! (Updated 10.25.2015) !!!'''
'''VERSION: 1.0.2 !!! (Updated 6.6.2016) !!!'''
'''Github Repo:''' Users can clone from github repository as well : [https://github.com/Santy-8128/m3vcftools m3vcftools Github]
'''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 !!!'''
! Download Link
! Download Link
|-
|-
| m3vcftools Source Files
| DosageConvertor Source Files
| [ftp://share.sph.umich.edu/m3vcftools/m3vcftools.v1.0.1.tar.gz UNIX Users ]
|
[ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertor.v1.0.2.tar.gz UNIX Users ]
|}
|}
= Usage=
= Usage=
Users should follow the following steps to compile '''m3vcftools ''' (if they downloaded the source files).
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 m3vcftools.v1.0.1.tar.gz
tar -xzvf DosageConvertor.v1.0.2.tar.gz
cd m3vcftools /
cd DosageConvertor/
make
make
For e.g. to calculate LD the command should be: <code>../bin/m3vcftools --vcf INPUT.m3vcf.gz --hap-r2 --ld-window-bp 10000 --min-r2 0.4 --out PREFIX</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].
