Required arguments

Home
This table shows the input arguments that you must supply in order for IMPUTE2 to run. These are just the minimum requirements; the program will not do anything useful unless you also supply other input options and/or data files.

Flag Default Description
-g <file>
REQUIRED unless -known_haps_g provided 		none File containing genotypes for a study cohort that you want to impute or phase. The format of this file is described on our file format webpage and is the same as the output format from our genotype calling program CHIAMO.

If you do not supply a file of unphased genotypes via this argument, you must supply a file of phased study haplotypes via the -known_haps_g option.
-m <file>
REQUIRED 		none Fine-scale recombination map for the region to be analyzed. This file should have three columns: physical position (in base pairs), recombination rate between current position and next position in map (in cM/Mb), and genetic map position (in cM). The file should also have a header line with an unbroken character string for each column (e.g., "position COMBINED_rate(cM/Mb) Genetic_Map(cM)").

All of our reference panel download packages come with appropriate recombination map files.
-int <lower> <upper>
REQUIRED 		none Genomic interval to use for inference, as specified by <lower> and <upper> boundaries in base pair position. The boundaries can be expressed either in long form (e.g., -int 5420000 10420000) or in exponential notation (e.g., -int 5.42e6 10.42e6). This option is particularly useful for restricting test jobs to small regions or splitting whole-chromosome analyses into manageable chunks, as discussed in the section on analyzing whole chromosomes.

IMPUTE2 requires that you specify an analysis interval in order to prevent accidental whole-chromosome analyses. If you want to impute a region larger than 7 Mb (which is not generally recommended), you must activate the -allow_large_regions flag.