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.

SEE ALSO

       https://genome.sph.umich.edu/wiki/Minimac4

COPYRIGHT

       Copyright  ©  2014-2018  Sayantan  Das, Christian Fuchsberger, David Hinds Mary Kate Wing,
       Goncalo Abecasis