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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:
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:
* '''Improved Speed - ''' Minimac4 is approximately '''6 times''' faster for 1000 Genomes Phase 1 and Phase 3 and '''2 times''' faster for the HRC reference panels at negligible fall in accuracy (details of accuracy for imputing into 10 European samples are given here). The speed can be further improved by tuning the approximation parameters (see below), but we recommend using the default values.
* '''Improved Speed - ''' Minimac4 is approximately '''6 times''' faster for 1000 Genomes Phase 1 and Phase 3 and '''2 times''' faster for the HRC reference panels at comparable accuracy (details of accuracy for imputing into 10 European samples are given here). The speed can be further improved by tuning the approximation parameters (see below), but we recommend using the default values.
* '''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 <code>--chunkLengthMb 20</code> and <code>--chunkLengthOverlapMb 3</code>, although we recommend using the default values.
* '''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 <code>--chunkLengthMb 20</code> and <code>--chunkLengthOverlapMb 3</code>, although we recommend using the default values.
