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, 19:22, 16 November 2012
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| ==== Chromosome X ==== | | ==== Chromosome X ==== |
| * --xStart and --xEnd specifies the start and end of non-pseudo-autosomal regions on chromosome X. These options should be specified when --fitX is used. | | * --xStart and --xEnd specifies the start and end of non-pseudo-autosomal regions on chromosome X. These options should be specified when --fitX is used. |
− | ==== Other Options ====
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− | * --LDwindow specifies the size of the window to calculate variants LD matrix. The default is 1MB.
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| === Handling Unrelated Individuals === | | === Handling Unrelated Individuals === |
| * To let Rare-Metal-Worker handle unrelated individuals, we just have to code the individuals as unrelated in PED file, or each individual belongs to a unique family. Then Rare-Metal-Worker will take care of the rest. | | * To let Rare-Metal-Worker handle unrelated individuals, we just have to code the individuals as unrelated in PED file, or each individual belongs to a unique family. Then Rare-Metal-Worker will take care of the rest. |