Minimac4

Minimac4 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3.

Installation

A prebuilt Linux x86 executable is available at https://github.com/statgen/Minimac4/releases/latest by downloading and running minimac4-{version}-Linux-x86_64.sh. Alternatively, you can build from source.

Prerequisites for building from source

Minimac4 requires GCC >= v5 or a compiler with full C++11 support. Automatic installation of Minimac4 requires cget and CMake >= v3.2.

Building from source

The simplest way to build the latest Minimac4 and its dependencies is to use cget:

cget install --prefix <install_prefix> statgen/Minimac4

Alternatively, you can build manually:

cd Minimac4
cget install -f ./requirements.txt                      # Install dependencies locally.
mkdir build && cd build                                 # Create out of source build directory.
cmake -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake .. # Configure project with dependency paths.
make                                                    # Build.
make install                                            # Install

To build and run tests from build directory:

# bcftools is required to run tests
cmake -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DBUILD_TESTS=ON ..
make
make CTEST_OUTPUT_ON_FAILURE=1 test

Since some users have reported issues with installing cget with pip, a cmake-only alternative for installing dependencies is available:

cmake -P dependencies.cmake deps/
mkdir build; cd build
cmake -DCMAKE_PREFIX_PATH=$(pwd)/../deps/ -DCMAKE_CXX_FLAGS="-I$(pwd)/../deps/include" ..
make
make install

Usage

See minimac4 --help for detailed usage.

A typical Minimac4 command line for imputation is as follows

minimac4 reference.msav target.vcf.gz > imputed.sav

Here reference.msav is a reference panel (e.g. 1000 Genomes download) compressed with MVCF encoding, target.vcf.gz is an indexed VCF containing phased genotype array data, and imputed.sav is the imputed output.

The file formats VCF, BCF, and SAV are supported for both input and output:

minimac4 reference.msav target.bcf -o imputed.bcf
minimac4 reference.msav target.vcf.gz -o imputed.vcf.gz

A sites-only file can be generated with:

minimac4 reference.msav target.bcf -o imputed.sav -s imputed.sites.vcf.gz

Meta-imputation with MetaMinimac2 requires --empirical-output (or -e) to be specified:

minimac4 reference.msav target.bcf -o imputed.dose.sav -e imputed.empirical_dose.sav

Reference Panel Creation

If an M3VCF file is already available, it can be converted to the new MVCF format with:

minimac4 --update-m3vcf reference.m3vcf.gz > reference.msav

Otherwise, phased VCFs containing the reference haplotypes can be compressed into an MVCF with:

minimac4 --compress-reference reference.{sav,bcf,vcf.gz} > reference.msav