minimac4(1)

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.