Panel merging options

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These options allow IMPUTE2 to efficiently combine two reference panels typed on partially overlapping sets of variants.

Flag	Default	Description
-merge_ref_panels		Tells the program to combine information across two reference panels using the approach described here.
-merge_ref_panels_output_ref <file>	none	Activates -merge_ref_panels and tells the program to store the merged panel in two output files: a legend file named <file>.legend and a haplotype file named <file>.hap.
-merge_ref_panels_output_gen <file>	none	Activates -merge_ref_panels and tells the program to store the merged panel in .gen format in an output file named <file>.gen.

NOTE: If you want IMPUTE2 to print a merged reference panel with buffer regions included, you should use one of the last two options together with the -include_buffer_in_output flag.

NOTE: You can see an example run that uses -merge_ref_panels here.