Pre-phasing options

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You can greatly speed up your imputation through a process called "pre-phasing". The idea of this approach is to first phase your GWAS genotypes, then use the estimated GWAS haplotypes to impute untyped variants from a reference panel. The options in this table activate the corresponding functionality in IMPUTE2. You can see how these options are applied in this example command.

Flag	Default	Description
-prephase_g		Tells IMPUTE2 to phase the genotypes in the -g file. The estimated haplotypes are printed to a dedicated output file named "[-o]_haps", where [-o] is the name supplied for the main output file. To avoid edge effects in downstream imputation, IMPUTE2 will extend the estimated haplotypes into the buffer regions that flank the main region specified via -int.
-use_prephased_g		Tells IMPUTE2 to perform imputation with pre-phased GWAS haplotypes, which must be supplied via a -known_haps_g file. This file will often be produced by a pre-phasing run that used -prephase_g on the same imputation interval (-int), although it may also come from a different phasing algorithm like SHAPEIT, which can print haplotypes in -known_haps_g format. We now recommend using SHAPEIT for pre-phasing and IMPUTE2 for downstream imputation.