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| <code>--refHaps ref.hap.gz </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/ MaCH download page])
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| <code>--vcfReference </code>
| <code>--vcfReference </code>
