Minimac3 - Full List of Options

Full List of Options

The following table gives a brief description of all the parameters of Minimac3. A detailed description would be available soon.

Parameter	Description
--refHaps filename	VCF file or M3VCF file containing haplotype data for reference panel.
--passOnly	If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on M3VCF files yet).
--haps filename	File containing haplotype data for target (gwas) samples. Must be a VCF file.
--processReference	This option will only convert an input VCF file to M3VCF format (maybe for a later run of imputation). If this option is ON, no imputation would be performed and thus all other parameters will be ignored (of course, except for parameters on Reference Haplotypes and Subsetting Options). This option also does parameter estimation using the reference panel and saves them in the M3VCF file (the estimation can be skipped with rounds = 0)
--prefix output	Prefix for all output files generated. By default: [Minimac3.Output]
--updateModel	If ON, saved parameter estimates read from a M3VCF file will be further updated using the gwas samples. Will be ignored if VCF reference file. [Default: OFF]
--nobgzip	If ON, output files will be NOT bgzipped.
--doseOutput	If ON, imputed data will be output as dosage file as well [Default: OFF].
--hapOutput	If ON, phased imputed data will be output as well [Default: OFF].
--format	Specifies which fields to output for the FORMAT field in output VCF file. Available handles: GT,DS,GP [Default: GT,DS].
--chr 22	Chromosome number for which we will carry out imputation.
--start 100000	Start position for imputation by chunking. Would not work without --chr option.
--end 200000	End position for imputation by chunking. Would not work without --chr option.
--window 5000	Length of buffer region on either side of --start and --end. By default = 0.
--rec	Recombination File from previous run of Minimac/Minimac3. (--err parameter must also be provided, if using this handle)
--err	Error File from previous run of Minimac/Minimac3. (--rec parameter must also be provided, if using this handle)
--rounds 5	Rounds of optimization for model parameters, which describe population recombination rates and per SNP error rates. By default = 5.
--states 200	Maximum number of reference (or target) haplotypes to be examined during parameter optimization. By default = 200.
--help	A short help on options.
--cpus 5	Number of cpus for parallel computing. Would work only with Minimac3-omp.
--noPhoneHome	If ON, code will NOT send a SUCCESS/FAILURE status of the execution to home server.
--phoneHomeThinning 50	Percentage probability of sending SUCCESS/FAILURE status of the execution to home server [Default: 50%]