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! Description
! Description
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|-
| <code>--refSnps ref.snps</code>
| <code>--refSnps ref.snps.gz </code>
| List of SNPs in the reference panel
| List of SNPs in the reference panel
|-
|-
| <code>--refHaps ref.hap</code>
| <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])
| 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</code>
| <code>--snps target.snps.gz </code>
| SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel.
| SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel.
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|-
| <code>--haps target.hap</code>
| <code>--haps target.hap.gz </code>
| Phased haplotypes where missing genotypes will be imputed.
| Phased haplotypes where missing genotypes will be imputed.
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|-
