Minimac3 - Full List of Options

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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%]