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Revision as of 10:22, 10 December 2014
, 10:22, 10 December 2014→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
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 --conf ${SS}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT}
* <code>${SS}/svtoolkit/bin/genomestrip.pl -run-discovery</code> runs the GenomeSTRiP Discovery Pipeline
* <code>${GC}/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>--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]].
* <code>--conf ${SS}/gotcloud.conf</code> points to the configuration file to use.
* <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).
** The configuration for this test was downloaded with the seqshop input files (same as other tutorials).
