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Running GotCloud Indel
== Running GotCloud Indel ==
${GC}/gotcloud indel --conf ${SS}/gotcloud.conf --numjobs 2 6 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
* <code>${GC}/gotcloud</code> runs GotCloud
* <code>indel</code> tells GotCloud you want to run the indel calling pipeline.
** 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
* <code>--out_diroutdir</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
If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off.
 
== Examining GotCloud indel Ouptut ==

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