Example command
IMPUTATION WITH MERGED REFERENCE PANELS
Many investigators have access to multiple reference panels that could inform their imputation analyses. For example, they might want to supplement the 1,000 Genomes haplotypes (which can be downloaded here) with dedicated sequencing data from a study population.
If you have two panels that have been phased and put into IMPUTE2's reference format (legend/haplotype file pairs), you can ask the program to merge them internally and impute your study genotypes by entering the following command, which uses example data that come with the program download:
./impute2 \
-merge_ref_panels \
-m ./Example/example.chr22.map \
-h ./Example/example.chr22.1kG.haps \
./Example/example.chr22.hm3.haps \
-l ./Example/example.chr22.1kG.legend \
./Example/example.chr22.hm3.legend \
-g ./Example/example.chr22.study.gens \
-strand_g ./Example/example.chr22.study.strand \
-int 20.4e6 20.5e6 \
-Ne 20000 \
-o ./Example/example.chr22.two.phased.impute2
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Comments
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For details on how the reference panel merging works, please read the documentation.
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This example tells the program to produce results for a 100 kb region (positions 20,400,000-20,500,000) on a single chromosome (IMPUTE2 assumes there is only one chromosome per input file, and that all input files in a single run come from the same chromosome). Applying the program to a much larger region—say, a whole chromosome or the whole genome—requires running many such jobs with different values of the -int parameter, usually in parallel on a computing cluster. For more details about how to do this, see here.
How to use example commands
All of the data files in the example command above are included in the Example/ directory that comes with the IMPUTE2 software download. You should run the command from the main download directory, which is the one that contains the impute2 executable. For example, if you just downloaded a software package named impute_v2.X.Y_i386.tgz and unpacked it according to the directions here, you can reach the appropriate directory by typing "cd impute_v2.X.Y_i386/" on the command line.
Once you have found the right directory, you should be able to run the example command by entering it into a Unix-style terminal window. Depending on the settings of your computer, this may be as simple as highlighting the command text in your web browser, using the browser's Copy command, and then using the Paste command in your terminal window. (You may then need to hit 'enter' to start the run.)
Note that most lines in the example command end with the '\' character. This is not actually part of the command; it is just a shorthand notation that means "keep reading the next line as part of a single command." We use this notation to split the command over multiple lines so it is easier to read. This is a valid way to enter commands in a Unix-style terminal window, but it would be equivalent to put all of the arguments on a single line, separated by spaces.
You do not have to run IMPUTE2 exactly as in the example. Some of the arguments shown here are optional, and there are many other options that could be added to modify the behavior of the program. For a full list of available options, see here.
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