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= Variant Calling Pipeline =
Back to parent: [[GotCloud]]
Back to parent: [[GotCloud]]
The Variant Calling Pipeline (UMAKE) takes recalibrated BAM files and detects SNPs and calls their genotypes, producing VCF files.
The Variant Calling Pipeline (UMAKE) takes recalibrated BAM files and detects SNPs and calls their genotypes, producing VCF files.
== Running the GotCloud Variant Calling Pipeline ==
The variant calling pipeline (umake) is run using the <code>umake.pl</code> script found in the <code>bin/</code> directory under the <code>gotcloud/</code> installation.
===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.
*Run variant calling pipeline test:
umake.pl --test OUTPUT_DIR
where OUTPUT_DIR is the directory where you want to store the test results
If you see "Successfully ran the test case, congratulations!", then you are ready to align samples.
== Overview of Mapping Pipeline Steps ==
Here is an overview of the Variant Calling Pipeline:
Here is an overview of the Variant Calling Pipeline:
