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

 

  time perl ${SS}/svtoolkit/bin/genomestrip.pl -run-discovery --metadata ${SS}/svtoolkit/metadata --conf ${SS}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT}

  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>${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>--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>--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 for this test was downloaded with the seqshop input files.

** The configuration for this test was downloaded with the seqshop input files (same as other tutorials).

* <code>--region 22:36000000-37000000</code>  

* <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

** 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

* <code>--base_prefix</code> tells the pipeline the prefix to append to relative paths.

** 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

* <code>--out_dir</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

--base_prefix tells GotCloud the prefix to append to relative paths.

** Based on <code>gotcloud.conf</code>, the GenomeSTRiP output will go in <code>$(OUT_DIR)/sv</code>

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

This will take ~2 minutes to finish.

This will take ~2-3 minutes to finish.

Let's see the final outputs produced.

Let's see the final outputs produced.

  less $OUT/sv/discovery/discovery.vcf

  less ${OUT}/sv/discovery/discovery.vcf

You will see output file that looks like this

You will see output file that looks like this