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Revision as of 17:09, 17 December 2014
, 17:09, 17 December 2014→What does a real SV look like?
Main Workshop wiki page: [[SeqShop: December 2014]]
Main Workshop wiki page: [[SeqShop: December 2014]]
See the [[Media:Seqshop cnv partb 2014 06.pdf|introductory slides]] for an intro to this tutorial.
See [[Media:Seqshop cnv partb 2014 06.pdf|lecture slides]] for the lecture slides associated with this tutorial.
== Goals of This Session ==
== Goals of This Session ==
== Setup in person at the SeqShop Workshop ==
== Setup in person at the SeqShop Workshop ==
''This section is specifically for the SeqShop Workshop computers.''
''This section is specifically for the SeqShop Workshop computers.''
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<div class="mw-collapsible mw-collapsed" style="width:600px">
''If you are not running during the SeqShop Workshop, please skip this section.''
''If you are not running during the SeqShop Workshop, please skip this section.''
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* Setup an output directory
* Setup an output directory
** It will leave your output directory from the previous tutorial in tact.
** It will leave your output directory from the previous tutorial in tact.
source /home/mktrost/seqshop/setup.txt
source /net/seqshop-server/home/mktrost/seqshop/setup.txt
* You won't see any output after running <code>source</code>
* You won't see any output after running <code>source</code>
** It silently sets up your environment
** It silently sets up your environment
** If you want to view the detail of the setup, type
** If you want to view the detail of the setup, type
less /home/mktrost/seqshop/setup.txt
less /net/seqshop-server/home/mktrost/seqshop/setup.txt
and press 'q' to finish.
and press 'q' to finish.
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</div>
</div>
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== Setup when running on your own outside of the SeqShop Workshop ==
== Setup when running on your own outside of the SeqShop Workshop ==
perl $GC/bin/genomestrip.pl
perl $GC/bin/genomestrip.pl
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<div class="mw-collapsible mw-collapsed">
''View Results''
''View Results''
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<div class="mw-collapsible-content">
ERROR: One of command options among --run-metadata, --run-discovery, --run-genotype, --run-thirdparty must be specified
ERROR: One of command options among --run-metadata, --run-discovery, --run-genotype, --run-thirdparty must be specified
ERROR: Missing required option, outdir
ERROR: Missing required option, outdir
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<div class="mw-collapsible-content" style="width:800px">
7 COHERENCE;COVERAGE;DEPTH;DEPTHPVAL
7 COHERENCE;COVERAGE;DEPTH;DEPTHPVAL
18 COHERENCE;COVERAGE;DEPTH;DEPTHPVAL;PAIRSPERSAMPLE
3 COHERENCE;COVERAGE;DEPTH;PAIRSPERSAMPLE
3 COHERENCE;COVERAGE;DEPTH;PAIRSPERSAMPLE
2 COHERENCE;COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE
2 COHERENCE;COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE
2 COVERAGE;DEPTH;PAIRSPERSAMPLE
2 COVERAGE;DEPTH;PAIRSPERSAMPLE
4 COVERAGE;DEPTHPVAL
4 COVERAGE;DEPTHPVAL
4 COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE
5 COVERAGE;PAIRSPERSAMPLE
5 COVERAGE;PAIRSPERSAMPLE
</div>
</div>
</div>
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== Starting SNP Call on your own Genome ==
== Return to Workshop Wiki Page ==
Return to main workshop wiki page: [[SeqShop: December 2014]]
