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Revision as of 23:18, 18 May 2015
, 23:18, 18 May 2015→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
${GC}/gotcloud genomestrip --run-discovery --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT}
* <code>${GC}/bin/genomestrip.pl -run-discovery</code> runs the GenomeSTRiP Discovery Pipeline
* <code>${GC}/gotcloud genomestrip -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]].
* <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 file cannot read environment variables, so we need to tell it the path to the input files, ${SS}
** The Configuration file cannot read environment variables, so we need to tell it the path to the input files, ${SS}
** Alternatively, gotcloud.conf could be updated to specify the full paths
** Alternatively, gotcloud.conf could be updated to specify the full paths
* <code>--out_dir</code> tells GotCloud where to write the output.
* <code>--outdir</code> tells GotCloud where to write the output.
** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line
** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line
** Based on <code>gotcloud.conf</code>, the GenomeSTRiP output will go in <code>$(OUT_DIR)/sv</code>
** Based on <code>gotcloud.conf</code>, the GenomeSTRiP output will go in <code>$(OUT_DIR)/sv</code>
