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Revision as of 10:14, 23 October 2014
, 10:14, 23 October 2014→Running the GotCloud Variant Calling Pipeline
= Running the GotCloud Variant Calling Pipeline =
= Running the GotCloud Variant Calling Pipeline =
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>.
==Running the Automatic Test==
==Running the Automatic Test==
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.
*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.
= Overview of Variant Calling Pipeline Steps =
= Overview of Variant Calling Pipeline Steps =
