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==Introduction==
Main Workshop wiki page: [[SeqShop: December 2014]]
See the [[Media:Seqshop cnv partb 2014 06.pdf|introductory slides]] for an intro to this tutorial.
== Goals of This Session ==
== Goals of This Session ==
* What we want to learn is calling large deletions using GenomeSTRiP implemented in [[GotCloud]] pipeline
* What we want to learn
** How to prepare metadata for running GenomeSTRiP.
** How to prepare metadata for running GenomeSTRiP.
** How to perform variant discovery and filtering for large deletions
** How to perform variant discovery and filtering for large deletions
** How to perform genotyping for large deletions
** How to perform genotyping for large deletions
** How to perform variant discovery and filtering from third party sites.
** How to perform variant discovery and filtering from third party sites.
== GenomeSTRiP ==
== GenomeSTRiP ==
== 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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''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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