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GotCloud BAM Index File
;Do you notice a difference between this index and yours?
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<li>Answer:</li>
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<li>It doesn't have a full path to the BAM file, while your index has /home/...</li>
[[File:Bamindex1.png|300px]]
<li>That's ok, we will use the <code>--base_prefix ${SS}</code> command-line option to prefix the BAM paths</li><li>Alternatively, we could have set BAM_INDEX in <code>gotcloud.conf</code> contains to the path to those the BAMs<pre>BAM_INDEX = /home/username/seqshop/example</pre> </li>[[File<ul><li>NOTE:BamindexConfthe conf file can't interpret ${SS} environment variables or '~', so you would have to specify the full path</li><li>We just used the command-line option for this tutorial since this path will vary by user.png|300px]]</li></ul>
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