Minimac3 Examples

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 is designed to give users a few examples on how to use Minimac3.

Examples

Here we give some examples of using Minimac3 for typical imputation experiments. Users should also check the wiki pages on Minimac3 Usage and Imputation Cookbook for further details on available parameter options and imputing GWAS samples.

All example data sets used below are available in the Minimac3 package available for download here. Users should follow the following steps to compile Minimac3 (after downloading it) and then move to directory Minimac3/test/ before running the examples given below.

## EXTRACT MINIMAC3 AND COMPILE
 
tar -xzvf Minimac3.v1.0.0.tar.gz
cd Minimac3/
make
cd test/

The following example uses a VCF reference file [refPanel.vcf] and a VCF target sample file [targetStudy.vcf]

 ../bin/Minimac3 --refHaps refPanel.vcf \ 
                 --haps targetStudy.vcf \
                 --prefix testRun

The following example is same as above but uses minimac3-omp (which is implemented using openMP programming enabling parallel computing).

 ../bin/Minimac3-omp --refHaps refPanel.vcf \
                     --haps targetStudy.vcf \
                     --prefix testRun \
                     --cpus 5

The following example converts a VCF reference file into M3VCF (only). It also does parameter estimation based on the reference panel using leave-one-out method and saves them in the M3VCF file. The parameter estimation can be skipped with "--rounds = 0". If the option "--processReference" is ON, no imputation will be done, only compression of file from VCF to M3VCF format will be done.

../bin/Minimac3 --refHaps refPanel.vcf \ 
                --processReference \ 
                --prefix testRun

The following example uses a M3VCF file (which was created in the previous example) and VCF target sample files (targetStudy.vcf) for imputation.

../bin/Minimac3 --refHaps testRun.m3vcf.gz \ 
                --haps targetStudy.vcf \ 
                --prefix testRun

[NOTE: In the example above, if testRun.m3vcf.gz was created with rounds = 0, it would contain no parameter estimates. Note that the program works with the saved estimates when available (as in the example above), whereas it does parameter estimation when the estimates are NOT available (as in the example below which is created with rounds = 0)]

../bin/Minimac3 --refHaps refPanel.vcf \ 
                --processReference \ 
                --rounds 0 \ 
                --prefix testRun
../bin/Minimac3 --refHaps testRun.m3vcf.gz \ 
                --haps targetStudy.vcf \ 
                --prefix testRun

The following example also uses a M3VCF reference file [refPanel.m3vcf.gz] and a VCF target sample file [targetStudy.vcf]. However, it only analyzes chromosome 6 from position 505988 to 873131 (allowing a buffer of 100 bp on either side). It also outputs a phased haplotype file (using --hapOutput, option) and the usual dosage file (using --doseOutput, option)

../bin/Minimac3 --refHaps testRun.m3vcf.gz \ 
                --haps targetStudy.vcf \
                --chr 6 \ 
                --start 505988 \ 
                --end 873131 \ 
                --window 100 \  
                --prefix testRun \ 
                --hapOutput \ 
                --doseOutput

For examples on imputation of chromosome X, see Chromosome X Imputation

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.

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:

• Minimac3 Overview Page

• Minimac3 Usage and Documentation

• Minimac3 Imputation Cookbook (Recommended for New Users!!)

• Chromosome X Imputation

• Minimac3 Examples

• M3VCF Files

Contact

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