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** How to examine the variants at particular genomic positions
** How to evaluate the quality of SNP calls
 
== Setup in person at the SeqShop Workshop ==
''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.''
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{{SeqShopLogin}}
=== Setup your run environment===This is the same setup you did for the previous tutorial, but you need to redo it each time you log in.
This is the same setup you did for the previous tutorial, but you need to redo it each time you log in. It will setup some environment variables to point you to:* [[GotCloud ]] program
* Tutorial input files
* Setup an output directory
* You won't see any output after running <code>source</code>
** It silently sets up your environment
** If you want to view the detail of the set upsetup, type
less /home/mktrost/seqshop/setup.txt
and press 'q' to finish.
 
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View setup.txt
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== Setup when running on your own outside of the SeqShop Workshop ==
''This section is specifically for running on your own outside of the SeqShop Workshop.''
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''If you are running during the SeqShop Workshop, please skip this section.''
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=== Download the example data ===
 
=== Setup your run environment ===
 
Environment variables will be used throughout the tutorial.
 
We recommend that you setup these variables so you won't have to modify every command in the tutorial.
 
 
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I'm using bash (replace the paths below with the appropriate paths):
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* Point to where you installed GotCloud
*:<pre>export GC=/home/username/gotcloud</pre>
* Point to where you installed the seqshop files
*:<pre>export SS=/home/username/seqshop/</pre>
* Point to where you want the output to go
*:<pre>export OUT=/home/username/seqshop_output/</pre>
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I'm using tcsh (replace the paths below with the appropriate paths):
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* Point to where you installed GotCloud
*:<pre>setenv GC /home/username/gotcloud</pre>
* Point to where you installed the seqshop files
*:<pre>setenv SS /home/username/seqshop/</pre>
* Point to where you want the output to go
*:<pre>setenv OUT /home/username/seqshop_output/</pre>
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== Examining GotCloud SnpCall Input files ==

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