The input file format, output file formats and typical command lines are same in Minimac4 (as they were in minimac3). Some of the main new features are summarized below:
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 ( larger chromosomes need the same amount of memory as smaller ones). The length of the chunk and the overlap can be controlled by the parameters <code>--chunkLengthMb</code> and <code>--chunkLengthOverlapMb</code>, although we recommend using the default values.
* '''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
levels of approximation will reduce the compute time but also marginally reduce the imputation accuracy. We recommend using the default values .
* '''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.
= Reference Panels for Download =