Introduction

Minimac3 is a lower memory and more computationally efficient implementation of minimac2. It is an algorithm for genotypic imputation that works on phased genotypes (say from MaCH) and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.

This wiki page gives users a summary of changes over the versions.

Change Log Summary

This section gives details of the changes over the different versions.

Minimac3 Changes:

1.0.10 (February 27, 2015)

Version : 1.0.10 Author : Sayantan Das Date : February 27, 2015

       Add parameter --log which will output a log file (BUT not print 
       on the screen). Also added legacy parameter --myChromosome whi-
       will enable users to use special chromosomes (apart from 1-22 
       and X)

Version : 1.0.8, 1.0.9 Author : Sayantan Das Date : February 20, 2015

       Removed dependcies on boost directory. Converted all double to fl-
       oat. Had to change the main imputation formula to work well for l-
       arge values. Also updated Rsq calulation formual to avoid underfl-
       as a result of using float. Made minor changes to memory allocati-
       on so as to remove all 2-d or 3-d look-ups. Updated a loop to rem-
       ove repeat allocation, similar to minimac2. Now it is faster and 
       uses much lesser memory.

Version : 1.0.7 Author : Sayantan Das Date : January 31, 2015

       Fixed minor bugs and made thigsn ready for final release !!!

Version : 1.0.6 Author : Sayantan Das Date : November 4, 2014

       Mended some minor bugs.

Version : 1.0.5 Author : Sayantan Das Date : October 3, 2014

       Implemented chromosome X imputation (both PAR and non-PAR). Also

added bgzip option to enable tabix options.

Version : 1.0.4 Author : Sayantan Das Date : September 19, 2014

       Improved the chuking option for the compressed files. Updated name

OPTM to M3VCF (Minimac3 VCF). Changed handle to --processReference. Added the option to add parameter estimates within M3VCF files wh- -ich can be used for later runs. Added a new handle --updateModel that will allow users to update these estimates using the target panel as well, if and when they think necessary.

Version : 1.0.2 Author : Sayantan Das Date : August 28, 2014

       Mended a bug related to --vcfoutput option when used with --gzip

option. Also added a option --format to manage handles in the FORMAT field for output VCF files.

Version : 1.0.1 Author : Sayantan Das Date : August 6, 2014

       Added the --window option that will allow a buffer region around

chunks. Also implemented this --start, --end and --window option on OPTM files. Minimac3 will, thus, be able to handle chunks on OPTM files as well. However, it will not perform the optimal all- -ocation again but just extract the chunk from the given file.

Version : 1.0.0 Author : Sayantan Das Date : July 21, 2014

       Added the --vcfOutput option that will output the dosage in VCF

format as well. Improved it by allowing to flush out VCF files after every 200 samples to save memory. Also implemented openmp to allow parallel computing.

Version : 0.7.1 Author : Sayantan Das Date : June 8, 2014

       Added the --golden option that can calculate the actual R-square

if the true/hard genotypes are provided in a vcf file. Made minor editions for debugging.

Version : 0.6.2 Author : Sayantan Das Date : June 8, 2014

       Edited bug in VCF packing part that was giving slightly less opt-

mized configurations.

Version : 0.6.1 Author : Sayantan Das Date : June 7, 2014

       Worked on an important bug that gave memory overflow in large sa-

mples. Name changed to Minimac3. Added utility for VCF output fo- rmat that would enable users to easy data manipulation.

Version : 0.5.1 Author : Sayantan Das Date : April 9, 2014

   	Removed futher bugs. Modified to use lesser memory and run faster.

The Unique.cpp file was updated according to Goncalo's packVcf so- ftware. Target Data is being read more effeciently. Scaffolding done locally during imputation. Changed name to Minimac2.

Version : 0.4.1 Author : Sayantan Das Date : March 14 2014

   	Removed bug with --sample. Added lots of other options like --chr,

--start, --end, --rounds, --states etc. Added data structure for variant type. Added structure so as NOT to use haplotype data after reading it once. Now the code uses the reduced haplotype structure once it has read the data. This was uses lesser memory.

Version : 0.2.1 Author : Sayantan Das Date : January 29 2014

Improved on the speed in parameter estimation part by NOT calcula- ting the optimal allocation everytime, instead update it from the original allocation. Updated to use --refSnps for reference, use --vcfTarget for target files.

Version : 0.1.1 Author : Sayantan Das Date : May 25 2013

   	Started working on the basis of code of minimac. Implemented State

Space Reduction Method for HMM calculations. Implemented the Para- meter Estimation part and Optimal Allocation part.

Download

Minimac3 is available as an undocumented release version. The source files (and binary executable) are available for download in Source Files and commonly used reference panels in VCF and M3VCF formats are available for download in Reference Panels.