Changes

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}

  ${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

* <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]].

** 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>

This will take ~2-3 minutes to finish.

This will take ~2-3 minutes to finish.