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Minimac4

1,029 bytes added, 01:57, 12 July 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 Improved Speed - ''' Minimac4 automatically chunks the whole chromosome (into overlapping chunks), analyzes each chunk sequentially is approximately '''6 times''' faster for 1000 Genomes Phase 1 and Phase 3 and then concatenates the imputed chunks back. This caps '''2 times''' faster for the memory usage across different chromosomes HRC reference panels at negligible fall in accuracy (larger chromosomes need the same amount details of memory as smaller onesaccuracy for imputing into 10 European samples are given here). The length of the chunk and the overlap speed can be controlled further improved by tuning the approximation parameters <code>--chunkLengthMb</code> and <code>--chunkLengthOverlapMb</code>(see below), although 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.  * '''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 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.
= Reference Panels for Download =
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