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Minimac

16 bytes added, 03:50, 12 October 2010
Running Minimac
! Description
|-
| <code>--refSnps ref.snps.gz </code>
| List of SNPs in the reference panel
|-
| <code>--refHaps ref.hap.gz </code>
| Reference haplotypes (e.g. from [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page])
|-
| <code>--snps target.snps.gz </code>
| SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel.
|-
| <code>--haps target.hap.gz </code>
| Phased haplotypes where missing genotypes will be imputed.
|-

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