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  • 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 m3vcftools users. Here are links to a few:

  • m3vcftools Overview Page


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.


m3vcftools is currently available as a pilot version. Please see our wiki page on m3vcftools Usage Options for more details on available options.

The software is in a very developmental mode and new options are going to be added regularly. Please join our NEW mailing list to get updates about future releases or provide us with feedback about possible bug reports, remarks on documentation, or new feature requests that you might want early. User could also email their queries/feedback to Sayantan Das.

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).

tar -xzvf m3vcftools.v1.0.1.tar.gz
cd m3vcftools /

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.