Minimac4

Introduction

Minimac4 is a latest version in the series of genotype imputation software - preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with negligible fall in imputation quality.

The Minimac3 mailing list has been renamed as the Minimac4 mailing list. If you were already a member, no need to re-join. If not, please join our mailing list to get updates about future releases or report possible bugs or email them to Sayantan Das.

Download

Minimac4 (version 1.0.2, updated 6.29.2017) is currently available for testing purposes only (while we still run more tests and wait on feedback about potential bugs). Commonly used reference panels in M3VCF format are available for download in Reference Panels.

Github Repo: : Minimac4 Github

What's New

The input file format, output file formats and typical command lines are same in Minimac4 (as they were in minimac3). Some of the main new features are summarized below:

• Automated Chunking - Minimac4 automatically chunks the whole chromosome (into overlapping chunks), analyzes each chunk sequentially and then concatenates the imputed chunks back. This caps the memory usage across different chromosomes (larger chromosomes need the same amount of memory as smaller ones). The length of the chunk and the overlap can be controlled by the parameters --chunkLengthMb and --chunkLengthOverlapMb, although we recommend using the default values.

• Approximations - Minimac4 uses some simple approximations to speed up the imputation analyses. The levels of approximation can be controlled by the parameters --probThreshold, --diffThreshold, and --topThreshold (details given in Minimac4 Usage). Higher levels of approximation will reduce the compute time but also marginally reduce the imputation accuracy. We recommend using the default values.

• Other Helpful Features
  • We introduced a parameter --memUsage that will estimate and report the memory required by the imputation experiment. This feature should be useful for users running their jobs on a compute cluster that requires memory specification.
  • We introduced some other FORMAT options for the output dosage data which should be sufficient to enable users to retrieve haplotype dosages, genotype probabilities, genotype dosages or any other measure of summary that they want.

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 (version 5)	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 (version 3)	1,092	VCF	-	1-22,X	Download
		M3VCF	YES	1-22,X	Download
			NO	1-22,X	Download
		VCF,M3VCF	YES	X	Download