Minimac4 Documentation

A typical Minimac4 command line would have the following parameter options:

      Reference Haplotypes : --refHaps [], --passOnly, --rsid,
                             --referenceEstimates [ON],
                             --mapFile [docs/geneticMapFile.b38.map.txt.gz]
         Target Haplotypes : --haps []
         Output Parameters : --prefix [Minimac4.Output], --estimate,
                             --nobgzip, --vcfBuffer [200], --format [GT,DS],
                             --allTypedSites, --meta, --memUsage
       Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb [3.00]
         Subset Parameters : --chr [], --start, --end, --window
  Approximation Parameters : --minimac3, --probThreshold [0.01],
                             --diffThreshold [0.01], --topThreshold [0.01]
          Other Parameters : --log, --help, --cpus [1], --params
                 PhoneHome : --noPhoneHome, --phoneHomeThinning [50]

Among all, --refHaps and --haps are required.

Reference Haplotypes

--refHaps <input_m3vcf_filename>

This option defines the reference panel in M3VCF format to impute against.

If your reference panel is in VCF format, please use Minimac3 to convert the VCF file to M3VCF (along with parameter estimation) and then use that M3VCF for imputation using Minimac4.

--passOnly

DEACTIVATED! If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on M3VCF files yet).

--rsid

If ON, Minimac4 will only import RS ID of variants from ID column of reference file (if available).

--referenceEstimates

ON by default. If ON, Minimac4 expects the input M3VCF file comes with parameter estimate; otherwise, a genetic map file for option --mapFile is required.

--mapFile <input_genetic_map_file>

This option is automatically ignored except when --referenceEstimates is OFF.

It defines the genetic map file used for recombination rate estimation during imputation.

The input genetic map file should be tab-separated, with 1st column as chromosome id, 3rd column as cumulative recombination rate in cM/Mb, and 4th as genetic map coordinates in cM.

Target Haplotypes

--haps <input_vcf_filename>

This option defines the pre-phased target genotype data in VCF format to impute.