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GotCloud: Alignment Pipeline (view source)

Revision as of 14:11, 26 February 2015

329 bytes added ,  14:11, 26 February 2015
→‎Recommended Settings
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==== Recommended Settings ====  
 
==== Recommended Settings ====  
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By default, the alignment pipeline uses bwa aln.  We recommend you use bwa mem instead.  To use that, set in your configuration file:
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As of GotCloud version 1.16, the alignment pipeline uses <code>bwa mem</code> by default.  Prior to version 1.16, the default aligner was <code>bwa aln</code>.   
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You can override the defaults by setting in your configuration file:
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* to use <code>bwa mem</code> (you do not need to set this in version 1.16 and later since it is the default)
 
  MAP_TYPE = BWA_MEM
 
  MAP_TYPE = BWA_MEM
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* to use <code>bwa aln</code> (you do not need to set this prior to version 1.16 since it is the default)
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MAP_TYPE = BWA
    
==== Additional Required Settings ====  
 
==== Additional Required Settings ====  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12939"

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