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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
perl ${GC}/bin/genomestrip.pl --run-discovery --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --numjobs 2 4 --conf ${SS}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT}
* <code>${GC}/bin/genomestrip.pl -run-discovery</code> runs the GenomeSTRiP Discovery Pipeline
* <code>--metadata ${SS}/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]].

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