minimac4 - Fast Imputation Based on State Space Reduction HMM

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

1.0.3                                               June 2022                                        MINIMAC4(1)

       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.

       minimac4 - Fast Imputation Based on State Space Reduction HMM

ReferenceHaplotypes--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).

   GWASHaplotypes--haps File containing haplotype data for target (gwas) samples.  Must  be  VCF  file.   Zipped  versions
              allowed.

   OutputParameters--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].

   SubsetParameters--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.

   OtherParameters--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.

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