Revision as of 19:05, 6 June 2016

Introduction

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK.

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

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

In case of any queries and bugs please contact Sayantan Das.

@@ Line 1: / Line 1: @@
-asafd
+* '''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
+ &nbsp;
+ 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].