---
name: "minimac4"
section: "1"
platform: "linux"
package: "minimac4"
version: "4.1.6-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/minimac4"
---

# minimac4(1)

Fast Imputation Based on State Space Reduction HMM

## NAME

minimac4 - Fast Imputation Based on State Space Reduction HMM

## DESCRIPTION

Minimac4 is a lower memory and more computationally efficient implementation of "minimac2/3".

It is an algorithm for genotypic imputation that works on phased genotypes (say from MaCH). Minimac4 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. This algorithm analyzes only the unique sets of haplotypes in small genomic segments, thereby saving on time-complexity, computational memory but no loss in degree of accuracy.

## OPTIONS

### Reference Haplotypes

- **--refHaps**

  M3VCF file containing haplotype data for reference panel.

- **--passOnly**

  This option only imports variants with FILTER = PASS.

- **--rsid**

  This option only imports RS ID of variants from ID column (if available).

### GWAS Haplotypes

- **--haps**

  File containing haplotype data for target (gwas) samples. Must be VCF file. Zipped versions allowed.

### Output Parameters

- **--prefix**

  Prefix for all output files generated. By default: \[Minimac4.Output\]

- **--processReference**

  This option will only convert an input VCF file to M3VCF format (currently de-activated in minimac4). If this option is ON, no imputation would be performed.

- **--nobgzip**

  If ON, output files will NOT be gzipped.

- **--format**

  Specifies which fields to output for the FORMAT field in output VCF file. Available handles: GT,DS,HDS,GP \[Default: GT,DS\].

- **--allTypedSites**

  If ON, sites available ONLY in GWAS panel will also be output \[Default: OFF\].

### Subset Parameters

- **--chr**

  Chromosome number for which to carry out imputation.

- **--start**

  Start position for imputation by chunking.

- **--end**

  End position for imputation by chunking.

- **--window**

  Length of buffer region on either side of **--start** and **--end**.

### Other Parameters

- **--log**

  If ON, log will be written to $prefix.logfile.

- **--help**

  If ON, detailed help on options and usage.

- **--cpus**

  Number of cpus for parallel computing. Works only with Minimac4-omp.

-

  ## SEE ALSO

**https://genome.sph.umich.edu/wiki/Minimac4**

## COPYRIGHT

Copyright © 2014-2018 Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo Abecasis