From Genome Analysis Wiki
* '''Automated Chunking - ''' Minimac4 automatically chunks the whole chromosome (into overlapping chunks), analyzes each chunk sequentially and then concatenates the imputed chunks back. This caps the memory usage across different chromosomes (memory requirement is based on chunk size, not chromosome size). The length of the chunk and the overlap can be controlled by the <code>--chunkLengthMb</code> and <code>--chunkLengthOverlapMb</code> options, although we recommend using the default values of 20 and 3, respectively.
* '''Approximations - ''' Minimac4 uses some simple approximations to speed up the imputation analyses. The levels of approximation can be controlled by the parameters <code>--probThreshold</code>, <code>--diffThreshold</code>, and <code>--topThreshold</code> (details given in Minimac4 Usage). Higher
values of approximation will reduce the compute time but also marginally reduce the imputation accuracy. We recommend using the default values ( = 0.01).
* '''Improved Chromosome X/Y Support - ''' Minimac4 can handle different ploidys in the same
GWAS file for imputation of sex chromosomes. For example, for the non-PAR region on chromosome X, males can imputed together with females, irrespective of whether males are coded as haploids or diploids. However, each sample must have a fixed ploidy. Thus, PAR and non-PAR regions still need to be imputed separately . But, males and females need not be separated. Please Chromosome X Imputation for more details.
* '''Other Helpful Features'''
** We introduced a parameter <code>--memUsage</code> that will estimate and report the memory required by
the imputation experiment. This feature should be useful for users running their jobs on a compute cluster that requires memory specification.** We introduced some other FORMAT options for the output dosage data which should be sufficient to enable users to retrieve haplotype dosages, genotype probabilities, genotype dosages or any other measure of summary that they want.
** We have fixed the bug related to FILTER=GENOTYPED and FILTER=GENOTYPED_ONLY which was causing a crash in bcftools.
* '''Obsolete Features'''
** In Minimac4, we removed the <code>--doseOutput</code> and <code>--hapOutput</code> options. Please use [[
DosageConvertor |DosageConvertor]] to convert your files to MaCH or PLINK dosage format.
** Currently Minimac4 can ONLY handle M3VCF format files. 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. The same holds for the option <code>--processReference</code> as well. Although the handle is made available, we will implement it in a later version.
** Parameters such as <code>--rounds</code>, <code>--states</code>, <code>--rec</code>, <code>--err</code> have been deactivated for now until we implement parameter estimation in minimac4.