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== using a VCF reference panel ==
== using a VCF reference panel ==
minimac --vcf --refHaps ref.vcf.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
minimac --vcfReference --refHaps ref.vcf.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
== using a MaCH reference panel ==
== using a MaCH reference panel ==
| Reference haplotypes (e.g. from [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page])
| Reference haplotypes (e.g. from [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page])
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|-
| <code>--vcf </code>
| <code>--vcfReference </code>
| This option specifies that the provided --refHaps file is provided in VCF format , no --refSNPs file needed.
| This option specifies that the provided --refHaps file is provided in VCF format , no --refSNPs file needed.
|-
|-
