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GotCloud: Amazon Demo (view source)

Revision as of 12:55, 31 October 2014

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__TOC__
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Back to [[GotCloud]]
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Back to [[GotCloud: Amazon]]
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== Introduction ==
 
== Introduction ==
 
This Amazon demo runs through the GotCloud SNP and INDEL calling pipelines.
 
This Amazon demo runs through the GotCloud SNP and INDEL calling pipelines.
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* [[SeqShop: Variant Calling and Filtering for INDELs Practical]]
 
* [[SeqShop: Variant Calling and Filtering for INDELs Practical]]
 
* [[SeqShop: Analysis of Structural Variation Practical]]
 
* [[SeqShop: Analysis of Structural Variation Practical]]
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To run this Demo on an Amazon Cluster rather than on a single node, see: [[StarCluster#Run_GotCloud_Demo_Using_StarCluster|StarCluster -> Run GotCloud Demo Using StarCluster]]
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== Starting up a Node ==
 
== Starting up a Node ==
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== Running the Demo on Already Running Node ==
 
== Running the Demo on Already Running Node ==
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=== Examine the Setup ===
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{{GotCloud: Amazon Demo Setup}}
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#After logging into the Amazon node as the ubuntu user, you should by default be in the ubuntu home directory: <code>/home/ubuntu</code>
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## You can check this by doing:
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##:<pre>pwd</pre>
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##* This should output: <code>/home/ubuntu</code>
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## Take a look at the contents of the ubuntu user home directory
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##: <pre>ls</pre>
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##* This should output be 2 directories, <code>example</code> and <code>gotcloud</code>
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##** The <code>example</code> directory contains the files for this demo
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##** The <code>gotcloud</code> directory contains the gotcloud programs and pre-compiled source
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#:[[File:DemoHome.png|400px]]
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# Look at the example input files:
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#:<pre>ls example</pre>
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#:[[File:ExampleFiles.png|400px]]
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#:# <code>bam.list</code> contains the list of BAM files per sample
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#:# <code>bams</code> is a subdirectory containing the BAM files for this demo
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#:# <code>test.bed</code> contains the region we want to process in this demo
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#:#* To make the demo run faster, we only want to process a small region of chromosome 22. This file tells GotCloud the region.  The region we are using is the APOL1 region
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#:#:[[File:BedContents.png|400px]]
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#:# <code>test.conf</code> contains the settings we want GotCloud to use for this run
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#:#:[[File:ConfContents.png|400px]]
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#:#:* For the demo, we want to tell GotCloud:
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#:#:*# The list of bams to use: <code>BAM_LIST = example/bam.list</code>
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#:#:*# The region to process rather than the whole genome: <code>UNIFORM_TARGET_BED = example/test.bed</code>
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#:#:*# The chromosomes to process.  The default chromosomes are 1-22 & X, but we only want to process chromosome 22: <code>CHRS = 22</code>
      
=== Run GotCloud SnpCall ===
 
=== Run GotCloud SnpCall ===
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# Look at the filtered file.
 
# Look at the filtered file.
 
#: <pre>zless -S output/vcfs/chr22/chr22.filtered.vcf.gz</pre>
 
#: <pre>zless -S output/vcfs/chr22/chr22.filtered.vcf.gz</pre>
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#: Scroll down some: [[File::SnpVcfOutput.png|700px]]
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#: Scroll down some: [[File:SnpVcfOutput.png|700px]]
 
## Check that GotCloud found the expected SNP at 22:36661906
 
## Check that GotCloud found the expected SNP at 22:36661906
 
##:<pre>tabix output/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 |head -1</pre>
 
##:<pre>tabix output/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 |head -1</pre>
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#:[[File::SnpTabix.png|700px]]
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#:[[File:SnpTabix.png|700px]]
 
# Look at the summary information
 
# Look at the summary information
 
#:<pre>cat output/vcfs/chr22/chr22.filtered.sites.vcf.summary</pre>
 
#:<pre>cat output/vcfs/chr22/chr22.filtered.sites.vcf.summary</pre>
 
#:[[File:SnpSummary.png|700px]]
 
#:[[File:SnpSummary.png|700px]]
 
#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''
 
#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''
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=== Run GotCloud Indel ===
 
=== Run GotCloud Indel ===
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==== Examining Indel Output ====
 
==== Examining Indel Output ====
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# Look inside the output directory to see the new indel directories:
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#:<pre>ls output</pre>
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#:[[File:IndelSnpOutput.png|900px]]
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#:#<code>aux</code> - intermediate indel files
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#:#<code>final</code> - final output of Indel pipeline
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#:#<code>indelvcf</code> - intermediate indel files
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#:#<code>gotcloud.indel.conf</code> - file containing all of the configuration settings used for this run of GotCloud
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#:#<code>gotcloud.indel.Makefile</code> - Makefile containing commands for this run of GotCloud
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#:#<code>gotcloud.indel.Makefile.log</code> - log of the GotCloud run
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# Important Indel output is in <code>output/final</code>
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#:<pre> ls output/final/</pre>
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#: [[File:IndelFinal.png|900px]]
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# Look at the final Indel VCF file.
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#: <pre>zless output/final/all.genotypes.vcf.gz</pre>
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#: Scroll down some: [[File::IndelLess.png|900px]]
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## Check that GotCloud found the expected Indel at 22:36662041
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##:<pre>tabix output/final/all.genotypes.vcf.gz 22:36662041-36662041|less -S</pre>
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##:[[File:IndelTabix.png|900px]]
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== Exit & Terminate ==
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Prior to terminating, make sure you copy any data off of the root EBS volume attached to the instance as it will be deleted when you terminate.
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# Exit from your terminal
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# Terminate your Amazon Instance
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#* Right click on the instance you want to terminate in the EC2 dashboard
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#* Select Terminate
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#* Select "Yes, Terminate" to indicate you would like to terminate and the storage will be deleted.
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