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, 15:56, 25 August 2015
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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 |
− | ${GC}/gotcloud genomestrip --run-discovery --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} --list bams/bam.list | + | ${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}/gotcloud genomestrip -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. |
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| ** 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> |
− | * <code>--list</code> tells GotCloud where to find <code>bam.list</code> relative to <code>outdir</code>.
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| This will take ~2-3 minutes to finish. | | This will take ~2-3 minutes to finish. |