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162 bytes added, 21:50, 29 June 2017
What's New
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 data imputed chunks back. This caps the memory usage across different chromosomes (large 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 the level levels of approximation will reduce the compute time but also marginally reduce the imputation accuracy. However, we We recommend using the default values which negligibly reduce the accuracy while still speeding the average compute time.
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