Minimac3 Examples

Examples

To look at the examples, the folder of Minimac3 needs to be copied to the users local directory first. Then move to the folder LocalDirectory/test/

 cp -r /net/fantasia/home/sayantan/Softwares/Minimac3/ LocalDirectoryMinimac3/
 cd LocalDirectoryMinimac3/test/

The following example uses a VCF reference file [refPanel.vcf] and a VCF target sample file [targetStudy.vcf]

 ../bin/Minimac3 --refHaps refPanel.vcf \ 
                 --haps targetStudy.vcf \
                 --prefix testRun

The following example is same as above but uses minimac3-omp (which is implemented using openMP programming enabling parallel computing).

 ../bin/Minimac3-omp --refHaps refPanel.vcf \
                     --haps targetStudy.vcf \
                     --prefix testRun \
                     --cpus 5

The following example converts a VCF reference file into M3VCF (only). It also does parameter estimation based on the reference panel using leave-one-out method and saves them in the M3VCF file. The parameter estimation can be skipped with "--rounds = 0". If the option "--processReference" is ON, no imputation will be done, only compression of file from VCF to M3VCF format will be done.

../bin/Minimac3 --refHaps refPanel.vcf \ 
                --processReference \ 
                --prefix testRun

The following example uses a M3VCF file (which was created in the previous example) and VCF target sample files (targetStudy.vcf) for imputation.

../bin/Minimac3 --refHaps testRun.m3vcf.gz \ 
                --haps targetStudy.vcf \ 
                --prefix testRun

[NOTE: In the example above, if testRun.m3vcf.gz was created with rounds = 0, it would contain no parameter estimates. Note that the program works with the saved estimates when available (as in the example above), whereas it does parameter estimation when the estimates are NOT available (as in the example below which is created with rounds = 0)]

../bin/Minimac3 --refHaps refPanel.vcf \ 
                --processReference \ 
                --rounds 0 \ 
                --prefix testRun
../bin/Minimac3 --refHaps testRun.m3vcf.gz \ 
                --haps targetStudy.vcf \ 
                --prefix testRun

The following example also uses a M3VCF reference file [refPanel.m3vcf.gz] and a VCF target sample file [targetStudy.vcf]. However, it only analyzes chromosome 6 from position 505988 to 873131 (allowing a buffer of 100 bp on either side). It also outputs a phased haplotype file (using --hapOutput, option) and the usual dosage file (using --doseOutput, option)

../bin/Minimac3 --refHaps testRun.m3vcf.gz \ 
                --haps targetStudy.vcf \
                --chr 6 \ 
                --start 505988 \ 
                --end 873131 \ 
                --window 100 \  
                --prefix testRun \ 
                --hapOutput \ 
                --doseOutput

For examples on imputation of chromosome X, see Chromosome X Imputation