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, 10:14, 23 October 2014
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| = Running the GotCloud Variant Calling Pipeline = | | = Running the GotCloud Variant Calling Pipeline = |
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− | The variant calling pipeline (umake) is run using <code>gotcloud snpcall</code> and <code>gotcloud ldrefine</code>. <code>gotcloud</code> is found under <code>gotcloud/</code>. | + | The variant calling pipeline (umake) is run using <code>gotcloud snpcall</code> and <code>gotcloud ldrefine</code>. |
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| ==Running the Automatic Test== | | ==Running the Automatic Test== |
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− | The automatic test runs the variant calling pipeline on a small testset and checks the results against expected results validating that GotCloud is installed correctly. | + | The automatic test runs the variant calling pipeline on a small test set and checks the results against expected results validating that GotCloud is installed correctly. |
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− | *Run variant calling pipeline test: | + | *Run <code>snpcall</code> pipeline test: |
| gotcloud snpcall --test OUTPUT_DIR | | gotcloud snpcall --test OUTPUT_DIR |
− | where OUTPUT_DIR is the directory where you want to store the test results | + | ** Where OUTPUT_DIR is the directory where you want to store the test results |
− | | + | ** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run snpcall on your own samples. |
− | If you see "Successfully ran the test case, congratulations!", then you are ready to run snpcall on your own samples. | + | *Run <code>ldrefine</code> pipeline test: |
| + | gotcloud snpcall --test OUTPUT_DIR |
| + | ** Where <code>OUTPUT_DIR</code> is the directory where you want to store the test results |
| + | ** If you see <code>Successfully ran the test case, congratulations!</code>, then you are ready to run ldrefine on your own samples. |
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| = Overview of Variant Calling Pipeline Steps = | | = Overview of Variant Calling Pipeline Steps = |