NPUTE
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A genotype imputation method based on K-nearest-neighbor and mismatch accumulator array.
There is a two step approach for the imputation method. As a fist step, testing is performed and a large number of windows is preferred to test. The best option for the actual run is to select the window with the highest estimated accuracy. More specifically, in the example data set the window that should be used for the actual permutation is window 12.
Quick Start
- To use NPUTE, import your data in csv format.
- Resources: NPUTEv1
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> npute. The input example data is called sample_data.csv, the testing_out.csv is the example output from the first step where we test for the optimum window. The Imputation_out.csv is the example output produced by the example data. |
Input File(s)
Use sample_data.csv from the directory above as test input.
Steps to run the App
When the app is run in the Discovery Environment, use the following steps with the above input file(s) to get the output provided in the next section below.
...
2nd step run the actual permutation
1.Select the file for the analysis(should be the same as in the previous step)
...
5. Under Output specify the output file name
6. Run the Imputation
Output File(s)
Expect as an output from the first step testing_out.txt. From the second step expect as an output Imputation_out.csv file.