DosageConvertor: Difference between revisions
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* '''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: 1.0.1 !!! (Updated 10.25.2015) !!!''' | |||
'''Github Repo:''' Users can clone from github repository as well : [https://github.com/Santy-8128/m3vcftools m3vcftools Github] | |||
'''Cloning from GitHub is recommened so that updates can be easily pulled back !!!''' | |||
{| class="wikitable" style="text-align:center" border="1" cellpadding="2" | |||
|- bgcolor="lightgray" | |||
! Description | |||
! Download Link | |||
|- | |||
| m3vcftools Source Files | |||
| [ftp://share.sph.umich.edu/m3vcftools/m3vcftools.v1.0.1.tar.gz UNIX Users ] | |||
|} | |||
= Usage= | |||
Users should follow the following steps to compile '''m3vcftools ''' (if they downloaded the source files). | |||
## EXTRACT M3VCFTOOLS AND COMPILE | |||
| |||
tar -xzvf m3vcftools.v1.0.1.tar.gz | |||
cd m3vcftools / | |||
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 convert a VCF file into M3VCF format : <code>../bin/m3vcftools --vcf INPUT.vcf.gz --recode --out PREFIX</code> | |||
= Contact = | |||
In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das]. | |||
Revision as of 19:05, 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: 1.0.1 !!! (Updated 10.25.2015) !!!
Github Repo: Users can clone from github repository as well : m3vcftools Github
Cloning from GitHub is recommened so that updates can be easily pulled back !!!
| Description | Download Link |
|---|---|
| m3vcftools Source Files | UNIX Users |
Usage
Users should follow the following steps to compile m3vcftools (if they downloaded the source files).
## EXTRACT M3VCFTOOLS AND COMPILE tar -xzvf m3vcftools.v1.0.1.tar.gz cd m3vcftools / make
For e.g. to calculate LD the command should be: ../bin/m3vcftools --vcf INPUT.m3vcf.gz --hap-r2 --ld-window-bp 10000 --min-r2 0.4 --out PREFIX
For e.g. to convert a VCF file into M3VCF format : ../bin/m3vcftools --vcf INPUT.vcf.gz --recode --out PREFIX
Contact
In case of any queries and bugs please contact Sayantan Das.
