Changes

* '''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 (memory requirement is based on chunk size, not chromosome size). The length of the chunk and the overlap can be controlled by the <code>--chunkLengthMb</code> and <code>--chunkLengthOverlapMb</code> options, although we recommend using the default values of 20 and 3, respectively.  

* '''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 (memory requirement is based on chunk size, not chromosome size). The length of the chunk and the overlap can be controlled by the <code>--chunkLengthMb</code> and <code>--chunkLengthOverlapMb</code> options, although we recommend using the default values of 20 and 3, respectively.  

* '''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 values of approximation will reduce the compute time but also marginally reduce the imputation accuracy. We recommend using the default values (= 0.01).

* '''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 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.

* '''Improved Chromosome X/Y Support - ''' Minimac4 can handle different ploidys in the same VCF file for imputation of sex chromosomes. For example, for the non-PAR region on chromosome X, males and females can be imputed together, 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. Please see Chromosome X Imputation for more details.

* '''Other Helpful Features'''

* '''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 a parameter <code>--memUsage</code> that will estimate and report the memory required by Minimac4. 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 introduced some other FORMAT options for the output dosage data, allowing 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.

** We have fixed the bug related to FILTER=GENOTYPED and FILTER=GENOTYPED_ONLY which was causing a crash in bcftools.

* '''Obsolete Features'''

* '''Obsolete Features'''

** In Minimac4, we removed the <code>--doseOutput</code> and <code>--hapOutput</code> options. Please use [[DosageConvertor |DosageConvertor]] to convert your files to MaCH or PLINK dosage format.

** In Minimac4, we removed the <code>--doseOutput</code> and <code>--hapOutput</code> options. Please use [[DosageConvertor]] to convert your files to MaCH or PLINK dosage format.

** Currently Minimac4 can ONLY handle M3VCF format files. If your reference panel is in VCF format, please use Minimac3 to convert the VCF file to M3VCF (along with parameter estimation) and then use that M3VCF for imputation using Minimac4. The same holds for the option <code>--processReference</code> as well. Although the handle is made available, we will implement it in a later version.

** Currently Minimac4 can ONLY handle M3VCF format files. If your reference panel is in VCF format, please use Minimac3 to convert the VCF file to M3VCF (along with parameter estimation) and then use that M3VCF for imputation using Minimac4. The same holds for the option <code>--processReference</code> as well. Although the handle is made available, we will implement it in a later version.

** Parameters such as <code>--rounds</code>, <code>--states</code>, <code>--rec</code>, <code>--err</code> have been deactivated for now until we implement parameter estimation in minimac4.

** Parameters such as <code>--rounds</code>, <code>--states</code>, <code>--rec</code>, <code>--err</code> have been deactivated for now until we implement parameter estimation in minimac4.