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:
* Minimac4 automatically chunks the whole chromosome (into overlapping chunks), analyzes each chunk and then concatenates the data back. This caps the memory usage across different chromosomes (large chromosomes need the same amount of memory as smaller ones). The length of the chunk and the overlap can be controlled by the parameters --chunkLengthMb and --chunkLengthOverlapMb
* Minimac4 uses some approximations to speed up the imputation analyses. The levels of approximation can be controlled by the parameters. Higher the level of approximation will reduce the compute time but also marginally reduce the imputation accuracy. However, we recommend using the default values which negligibly reduce the accuracy while still speeding the average compute time.