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| <code>--haps target.hap.gz </code>
| <code>--haps target.hap.gz </code>
| Phased haplotypes where missing genotypes will be imputed.
| Phased haplotypes where missing genotypes will be imputed.
|-
| <code>--sample target.sample </code>
| Sample list in ShapeIT format.
|-
| <code>--shape_haps target.hap.gz </code>
| ShapeIT phased haplotypes where missing genotypes will be imputed.
|-
| <code>--chr 22</code>
| Chromosome for which we will carry out imputation (needed to run ShapeIT with chr:pos identifiers - default setting).
|-
|-
| <code>--rounds 5</code>
| <code>--rounds 5</code>
