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The following example uses a VCF reference file <font face=Courier>[refPanel.vcf]</font> and a VCF target sample file <font face=Courier>[targetStudy.vcf]</font>
The following example uses a VCF reference file <font face=Courier>[refPanel.vcf]</font> and a VCF target sample file <font face=Courier>[targetStudy.vcf]</font>
../bin/Minimac3 --refHaps refPanel.vcf --haps targetStudy.vcf --prefix testRun
../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).
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
../bin/Minimac3-omp --refHaps refPanel.vcf \
--haps targetStudy.vcf \
--prefix testRun \
--cpus 5
The following example converts a VCF reference file into <font face=Courier>M3VCF</font> (only). It also does parameter estimation based on the reference panel using leave-one-out method and saves them in the <font face=Courier>M3VCF</font> file. The parameter estimation can be skipped with "<font face=Courier>--rounds = 0</font>". If the option "<font face=Courier>--processReference</font>" is ON, no imputation will be done, only compression of file from VCF to <font face=Courier>M3VCF</font> format will be done.
The following example converts a VCF reference file into <font face=Courier>M3VCF</font> (only). It also does parameter estimation based on the reference panel using leave-one-out method and saves them in the <font face=Courier>M3VCF</font> file. The parameter estimation can be skipped with "<font face=Courier>--rounds = 0</font>". If the option "<font face=Courier>--processReference</font>" is ON, no imputation will be done, only compression of file from VCF to <font face=Courier>M3VCF</font> format will be done.
../bin/Minimac3 --refHaps refPanel.vcf --processReference --prefix testRun
../bin/Minimac3 --refHaps refPanel.vcf \
--processReference \
--prefix testRun
The following example uses a <font face=Courier>M3VCF</font> file (which was created in the previous example) and VCF target sample files (<font face=Courier>targetStudy.vcf</font>) for imputation.
The following example uses a <font face=Courier>M3VCF</font> file (which was created in the previous example) and VCF target sample files (<font face=Courier>targetStudy.vcf</font>) for imputation.
../bin/Minimac3 --refHaps testRun.m3vcf.gz --haps targetStudy.vcf --prefix testRun
../bin/Minimac3 --refHaps testRun.m3vcf.gz \
--haps targetStudy.vcf \
--prefix testRun
[NOTE: In the example above, if <code>testRun.m3vcf.gz</code> was created with <code>rounds = 0</code>, 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 <code>rounds = 0</code>)]
[NOTE: In the example above, if <code>testRun.m3vcf.gz</code> was created with <code>rounds = 0</code>, 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 <code>rounds = 0</code>)]
../bin/Minimac3 --refHaps refPanel.vcf --processReference --rounds 0 --prefix testRun
../bin/Minimac3 --refHaps refPanel.vcf \
../bin/Minimac3 --refHaps testRun.m3vcf.gz --haps targetStudy.vcf --prefix testRun
--processReference \
--rounds 0 \
--prefix testRun
../bin/Minimac3 --refHaps testRun.m3vcf.gz \
--haps targetStudy.vcf \
--prefix testRun
The following example also uses a <font face=Courier>M3VCF</font> reference file <font face=Courier>[refPanel.m3vcf.gz]</font> and a VCF target sample file <font face=Courier>[targetStudy.vcf]</font>. 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 <code>--hapOutput,</code> option) and the usual dosage file (using <code>--doseOutput,</code> option)
The following example also uses a <font face=Courier>M3VCF</font> reference file <font face=Courier>[refPanel.m3vcf.gz]</font> and a VCF target sample file <font face=Courier>[targetStudy.vcf]</font>. 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 <code>--hapOutput,</code> option) and the usual dosage file (using <code>--doseOutput,</code> option)
../bin/Minimac3 --refHaps testRun.m3vcf.gz --chr 6 --start 505988 --end 873131 --window 100 --haps targetStudy.vcf --prefix testRun --hapOutput --doseOutput
../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|Chromosome X Imputation]]
For examples on imputation of chromosome X, see [[#Chromosome X Imputation|Chromosome X Imputation]]
