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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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| | #:[[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 ===
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| − | Now that we have examined the instance files, run GotCloud indel
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| − | # <pre>gotcloud indel --conf example/test.conf --outdir output --numjobs 8</pre>
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| − | #* The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found
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| − | #: [[File:RunIndel.png|700px]]
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| − | #:* This will take a few minutes to run.
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| − | #:* GotCloud first generates a makefile, and then runs the makefile
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| − | # When complete, GotCloud indel will indicate success/failure
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| − | #:[[File:IndelSuccess.png|700px]]
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| − | ==== 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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