Minimac3 - Full List of Options

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Introduction

Minimac3 is a lower memory and more computationally efficient implementation of minimac2. It is an algorithm for genotypic imputation that works on phased genotypes (say from MaCH) and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.

This wiki page gives users a full list of all the available options on Minimac3.

Full List of Options

The following table gives a brief description of all the parameters of Minimac3. A more detailed description would be available soon. Users should see the wiki-page on Minimac3 Usage and Documentation and Minimac3 Imputation Cookbook for further help on how to use these options.

Parameter Description
--refHaps filename VCF file or M3VCF file containing haplotype data for reference panel.
--rsid This option only imports RS ID of variants from ID column of reference file (if available).
--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.
--vcfOutput If ON, imputed data will NOT be output as VCF output file [Default: ON].
--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]
--allTypedSites Also Includes variants that were genotyped but NOT in the reference panel in the output files (and imputes any missing data in such variants to the major allele frequency).
--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 (in bp units) on either side of --start and --end. By default = 500000 (if chunking is done) and = 0 (if no chunking is being done).
--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.
--lowMemory If ON, a low memory version of Minimac3 will be run.
--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%]

Download

Minimac3 is available as an undocumented release version. The source files (and binary executable) are available for download in Source Files and commonly used reference panels in VCF and M3VCF formats are available for download in Reference Panels.

Useful Wiki Pages

There are a few pages in this Wiki that may be useful to for Minimac3 users. Here are links to a few:

Contact

In case of any queries and bugs please contact Sayantan Das.