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, 10:22, 10 December 2014
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| 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 |
− | time perl ${SS}/svtoolkit/bin/genomestrip.pl -run-discovery --metadata ${SS}/svtoolkit/metadata --conf ${SS}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} | + | 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). |