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Revision as of 13:12, 7 March 2013
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== Running the GotCloud Variant Calling Pipeline ==
== 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.
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>.
===Running the Automatic Test===
===Running the Automatic Test===
*Run variant calling pipeline test:
*Run variant calling pipeline test:
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
== Overview of Mapping Pipeline Steps ==
== Overview of Variant Calling Pipeline Steps ==
Here is an overview of the Variant Calling Pipeline:
Here is an overview of the Variant Calling Pipeline:
The BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls.
The BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls.
FASTQs can be converted to this type of BAM using the [[Mapping Pipeline]].
FASTQs can be converted to this type of BAM using the [[Alignment Pipeline]].
=== Index File ===
=== Index File ===
== Running ==
== Running ==
Running umake is straightforward:
Running variant calling is straightforward:
<code>
<code>
'''/usr/local/biopipe/bin/umake.pl --conf umake.conf --snpcall --numjobs 2
'''gotcloud snpcall --conf vc.conf --numjobs 2
'''gotcloud ldrefine --conf vc.conf --numjobs 2
</code>
</code>
Replace umake.conf with the approprate path/name of the user's configuration file.
Replace vc.conf with the approprate path/name of the user's configuration file.
If <code>OUT_DIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory.
If <code>OUT_DIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory.
To run on the Cluster, the following settings need to be added to the configuration file:
To run on the Cluster, the following settings need to be added to the configuration file:
TODO: COMING SOON
SLEEP_MULT = 20
SLEEP_MULT = 20
REMOTE_PREFIX = # REMOTE_PREFIX : Set if cluster node see the directory differently (e.g. /net/mymachine/[original-dir])
REMOTE_PREFIX = # REMOTE_PREFIX : Set if cluster node see the directory differently (e.g. /net/mymachine/[original-dir])
=== Results ===
=== Results ===
