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SeqShop: Calling Your Own Genome, May 2015 (view source)

Revision as of 23:25, 18 May 2015

1,601 bytes removed ,  23:25, 18 May 2015
→‎Start SNP Calling
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<div class="mw-collapsible" style="width:500px">
 
<div class="mw-collapsible" style="width:500px">
   −
=== Start SNP Calling ===
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=== Start INDEL Calling ===
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
==== Resume screen ====
 
==== Resume screen ====
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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).
   −
==== GotCloud SnpCall Configuration ====
+
==== GotCloud INDEL Configuration ====
    
  cat ~/$SAMPLE/gotcloud.conf
 
  cat ~/$SAMPLE/gotcloud.conf
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You will see something like this:
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Same as it looked yesterday with no special Configuration settings for INDEL calling.
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<pre>
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# Cluster Settings
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BATCH_TYPE =
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BATCH_OPTS =
     −
OUT_DIR = Sample13/output
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==== Running INDEL ====
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Run GotCloud indel with 8 jobs running in parallel
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# Align Settings
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* Why 8?   
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MAP_TYPE = BWA_MEM
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BWA_THREADS = -t 24
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FASTQ_LIST = fastq.list
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# SNP Call Settings
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UNIT_CHUNK = 20000000      # Chunk size of SNP calling : 20Mb
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VCF_EXTRACT = /net/seqshop-server/home/mktrost/seqshop/singleSample/snpOnly.vcf.gz
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MODEL_GLFSINGLE = TRUE
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MODEL_SKIP_DISCOVER = FALSE
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MODEL_AF_PRIOR = TRUE
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EXT_DIR = /net/seqshop-server/home/mktrost/seqshop/singleSample/ext
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EXT = $(EXT_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(EXT_DIR)/chrCHR.filtered.sites.vcf.gz
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</pre>
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===== Configuration Updates =====
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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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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 other than OUT_DIR, 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
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nedit $SAMPLE/gotcloud.conf&
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* Edit OUT_DIR
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OUT_DIR = Sample##/output
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* Save, and close
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  −
==== Running SnpCall ====
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Run GotCloud snpcall with 6 jobs running in parallel
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* Why 6?   
   
** You want to run as many as you can.
 
** You want to run as many as you can.
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** 5 of you on the machine - 5*6 = 30 jobs will be running in parallel on that machine
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** 3 of you on the machine - 3*8 = 24 jobs will be running in parallel on that machine
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  ${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 6
+
  ${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 8
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* Only need the configuration & number of threads, rest is specified within the configuration.
+
* Only need the configuration, number of threads, and the output directory, rest is specified within the configuration.
    
This will run overnight.  We will check if it completed at the practical in the morning.
 
This will run overnight.  We will check if it completed at the practical in the morning.
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13332"

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