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Running GotCloud/GenomeSTRiP Discovery Pipeline
To discover large deletions from the 62 BAMs we are using for this workshop, you can run the following command
time perl ${SSGC}/svtoolkit/bin/genomestrip.pl --run-discovery --metadata ${SS}/svtoolkitmetadata --conf ${SS}/metadata gotcloud.conf --numjobs 2 --conf ${SS}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT}* <code>${SSGC}/svtoolkit/bin/genomestrip.pl -run-discovery</code> runs the GenomeSTRiP Discovery Pipeline* <code>--metadata ${SS}/svtoolkit/metadata</code> points to the pre-made metadata file as explained in the previous section, [[#Running GotCloud/GenomeSTRiP Metadata Pipeline|Running GotCloud/GenomeSTRiP Metadata Pipeline]].
* <code>--conf ${SS}/gotcloud.conf</code> points to the configuration file to use.
** The configuration for this test was downloaded with the seqshop input files (same as other tutorials).

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