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SeqShop: Calling Your Own Genome, December 2014 (view source)

Revision as of 10:51, 10 December 2014

445 bytes added ,  10:51, 10 December 2014
→‎Configuring SnpCall
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* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
 
* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
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==== Configuring SnpCall ====
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==== GotCloud SnpCall Configuration ====
    
  cat ~/$SAMPLE/gotcloud.conf
 
  cat ~/$SAMPLE/gotcloud.conf
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===== Configuration Updates =====
 
===== Configuration Updates =====
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In order to complete SnpCall overnight, we are going to tell GotCloud to only call SNPs for the EXOME regions.
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'''No configuration updates from the original settings are necessary.'''
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* Originally you were going to update the configuration to do exome calling only, but we have decided to do whole genome
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** If it doesn't finish tonight, we will kill it at the tutorial in the morning, and take advantage of the GotCloud restart capability after the tutorial tomorrow.
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Edit  
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If you started making updates to your configuration yesterday, you can try to make it match above (mktrost is actually the path you want in the paths above).
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* The only difference from above should be your OUT_DIR.
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Check it with (leave as ~mktrost - you are comparing to my NA12878 conf file):
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  diff $SAMPLE/gotcloud.conf ~mktrost/NA12878/gotcloud.conf
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'''If you see differences, you can modify your file using nedit (or your favorite editor as you used yesterday).'''
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* '''Or you can copy my file and just change OUT_DIR:'''
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cp ~mktrost/NA12878/gotcloud.conf $SAMPLE/gotcloud.conf
 
  nedit $SAMPLE/gotcloud.conf&
 
  nedit $SAMPLE/gotcloud.conf&
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* Or you can use <code>vi</code> or <code>emacs</code> or your favorite editor
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* Edit OUT_DIR
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  OUT_DIR = Sample##/output
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Specify the target region:
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* Save, and close
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  UNIFORM_TARGET_BED = /net/seqshop-server/home/mktrost/seqshop/singleSample/20130108.exome.targets.bed
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* See [http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline#Targeted.2FExome_Sequencing_Settings|Targeted/Exome Sequencing Settings] for more information on the GotCloud configuration settings for running Targeted/Exome runs.
      
==== Running SnpCall ====
 
==== Running SnpCall ====
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12305"

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