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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]]
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]]
== Starting up a Node ==
== Starting up a Node ==
#:[[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]]'''
=== Run GotCloud Indel ===
Now that we have examined the instance files, run GotCloud indel
# <pre>gotcloud indel --conf example/test.conf --outdir output --numjobs 8</pre>
#* 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
#: [[File:RunIndel.png|700px]]
#:* This will take a few minutes to run.
#:* GotCloud first generates a makefile, and then runs the makefile
# When complete, GotCloud indel will indicate success/failure
#:[[File:IndelSuccess.png|700px]]
==== Examining Indel Output ====
# Look inside the output directory to see the new indel directories:
#:<pre>ls output</pre>
#:[[File:IndelSnpOutput.png|900px]]
#:#<code>aux</code> - intermediate indel files
#:#<code>final</code> - final output of Indel pipeline
#:#<code>indelvcf</code> - intermediate indel files
#:#<code>gotcloud.indel.conf</code> - file containing all of the configuration settings used for this run of GotCloud
#:#<code>gotcloud.indel.Makefile</code> - Makefile containing commands for this run of GotCloud
#:#<code>gotcloud.indel.Makefile.log</code> - log of the GotCloud run
# Important Indel output is in <code>output/final</code>
#:<pre> ls output/final/</pre>
#: [[File:IndelFinal.png|900px]]
# Look at the final Indel VCF file.
#: <pre>zless output/final/all.genotypes.vcf.gz</pre>
#: Scroll down some: [[File::IndelLess.png|900px]]
## Check that GotCloud found the expected Indel at 22:36662041
##:<pre>tabix output/final/all.genotypes.vcf.gz 22:36662041-36662041|less -S</pre>
##:[[File:IndelTabix.png|900px]]
== Exit & Terminate ==
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.
# Exit from your terminal
# Terminate your Amazon Instance
#* Right click on the instance you want to terminate in the EC2 dashboard
#* Select Terminate
#* Select "Yes, Terminate" to indicate you would like to terminate and the storage will be deleted.
