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Revision as of 11:41, 27 June 2014
, 11:41, 27 June 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
time perl ${SS}/svtoolkit/bin/genomestrip.pl -run-discovery --metadata ${SS}/svtoolkit/metadata --out ${OUT}/sv --conf ${SS}/gotcloud.conf --region 22:36000000-37000000 --numjobs 2 --gs-dir ${SS}/svtoolkit --index ${OUT}/bam.index --base-prefix ${SS}
* <code>${SS}/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>--out ${OUT}/sv</code> tells the pipeline where to put it's output (in an <code>sv</code> sub-directory of ${OUT}
* <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.
* <code>--region 22:36000000-37000000</code>
** The sample files are just a small region of chromosome 22, so to save time, we tell the pipeline to ignore the other regions
* <code>--numjobs</code> tells GotCloud how many jobs to run in parallel
** Depends on your system
* <code>--gs-dir ${SS}/svtoolkit</code>
--base_prefix tells GotCloud the prefix to append to relative paths.
The Configuration file cannot read environment variables, so we need to tell GotCloud the path to the input files, ${SS}
Alternatively, gotcloud.conf could be updated to specify the full paths
--out_dir 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
time perl ${GC}/bin/genomestrip.pl -run-discovery --metadata ${SS}/svtoolkit/metadata --out ${OUT}/sv --conf ${SS}/gotcloud.conf --region 22:36000000-37000000 --numjobs 2 --gs-dir ${SS}/svtoolkit
time perl ${GC}/bin/genomestrip.pl -run-discovery --metadata ${SS}/svtoolkit/metadata --out ${OUT}/sv --conf ${SS}/gotcloud.conf --region 22:36000000-37000000 --numjobs 2 --gs-dir ${SS}/svtoolkit
