M3vcftools
- Download Pilot Version 1.0.1 !!! (Updated Oct 2015) !!! See ChangeLog for details !!!
- Please join our NEW mailing list to get updates about future releases, bug fixes or post queries.
Useful Wiki Pages
There are a few pages in this Wiki that may be useful to for Minimac3 users. Here are links to a few:
Introduction
m3vcftools is a tool (exactly similar to vcftools) but will be much faster and can be used for simple data query and basic summary like allele frequency, linkage-r2 calculation, etc. m3vcftools is ideal for mega reference panels like Haplotye Reference Consortium (HRC) with over 32,000 samples where m3vcftools is 70-90 times faster than vcftools (18 mins vs 28 hours) in calculating AF or LD summaries. For panels like 1000 Genomes Phase 3, m3vcftools is 12-15 times faster.
The command line format for m3vcftools is going to be exactly same as that of vcftools, thus users wouldn't have to learn a new tool or change their already existing pipelines. The only difference would lie in the fact that m3vcftools usually takes M3VCF files has input instead of VCF files. Of course, the tool itself can convert a VCF file into M3VCf format which can then later be used for fast data query and summary statistics calculations.
Download
Minimac3 is currently available as a release version. Commonly used reference panels in M3VCF format are available for download in Reference Panels.
Please join our NEW mailing list to get updates about future releases or report possible bugs or email them to Sayantan Das.
VERSION: 1.0.13 !!! (Updated 10.15.2015) !!!
Github Repo: Users can clone from github repository as well : Minimac3 Github
Cloning from GitHub is recommened so that updates can be easily pulled back !!!
| Description | Download Link |
|---|---|
| Minimac3 Source Files | UNIX Users |
Usage
Users should follow the following steps to compile Minimac3 (if they downloaded the source files) or should skip them (if they downloaded the binary executable).
## EXTRACT MINIMAC3 AND COMPILE tar -xzvf Minimac3.v1.0.13.tar.gz cd Minimac3/ make
A typical Minimac3 command line for imputation is as follows
../bin/Minimac3 --refHaps refPanel.vcf \
--haps targetStudy.vcf \
--prefix testRun
Here refPanel.vcf is the reference panel used in VCF format (e.g. 1000 Genomes), targetStudy.vcf is the phased GWAS data in VCF format, and testRun is the prefix for the output files. Some commonly used reference panels are available for download in Reference Panels. See wiki page on Detailed Usage and Imputation Cookbook for further details on using Minimac3 for imputation analysis.
Users can always type the following for further support:
/bin/Minimac3 --help
Reference Panels for Download
Some commonly used reference panels are available for download here:
| Reference Panel | Number of Samples |
File Format | Parameter Estimates Available |
Chromosomes | Link |
|---|---|---|---|---|---|
| 1000 Genomes Phase 3 |
2,504 | VCF | - | 1-22,X | Download |
| M3VCF | YES | 1-22,X | Download | ||
| NO | 1-22,X | Download | |||
| VCF,M3VCF | YES | X | Download | ||
| 1000 Genomes Phase 1 |
1,092 | VCF | - | 1-22,X | Download |
| M3VCF | YES | 1-22,X | Download | ||
| NO | 1-22,X | Download | |||
| VCF,M3VCF | YES | X | Download |
Contact
In case of any queries and bugs please contact Sayantan Das.
