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Back to [[GotCloud]]
== Starting GotCloud AMI ==
Back to [[GotCloud: Amazon]]
The GotCloud AMI has the Demo data built into it.
== Introduction ==
This Amazon demo runs through the GotCloud SNP and INDEL calling pipelines.
The data used for this demo is originally from our sequencing workshop demos. We also have alignment and structural variation demos.
Links to the general GotCloud Demos (originally from our sequencing workshop):
* [[SeqShop: Sequence Mapping and Assembly Practical]]
* [[SeqShop: Variant Calling and Filtering for SNPs Practical]]
* [[SeqShop: Variant Calling and Filtering for INDELs 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 ==
See [[Amazon Single Node]] for instructions on starting a node and getting a terminal running.
* For the demo, we recommend using a <code>c3.2xlarge</code> instance.
== Running the Demo on Already Running Node ==
{{GotCloud: Amazon Demo Setup}}
=== Run GotCloud SnpCall ===
Now that we have examined the instance files, run GotCloud snpcall
# <pre>gotcloud snpcall --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:RunSnpCall.png|700px]]
#:* This will take a few minutes to run.
#:* GotCloud first generates a makefile, and then runs the makefile
#:* After a while GotCloud snpcall will print some messages to the screen. This is expected and ok.
# When complete, GotCloud snpcall will indicate success/failure
#:[[File:SnpcallSuccess.png|700px]]
==== Examining SnpCall Output ====
# ls on the ubuntu home directory to see the new output directory:
#:<pre>ls</pre>
#:[[File:SnpCallOutput1.png|500px]]
# Look inside the output directory:
#:<pre>ls output</pre>
#:[[File:SnpCallOutput2.png|700px]]
#:#<code>glfs</code> - intermediate per sample genotype likelihood files
#:#<code>jobfiles</code> - empty; was used to store commands as GotCloud was running
#:#<code>pvcfs</code> - intermediate vcfs with per sample information
#:#<code>split</code> - contains per chromosome directories with vcfs containing PASS only snps split up as required for beagle (part of ldrefine)
#:#<code>target</code> - contains the bed with the region to be processed
#:#<code>umake.snpcall.conf</code> - file containing all of the configuration settings used for this run of GotCloud
#:#<code>umake.snpcall.Makefile</code> - Makefile containing commands for this run of GotCloud
#:#<code>umake.snpcall.Makefile.cluster</code> - Makefile log of start/stop times of various steps
#:#<code>umake.snpcall.Makefile.log</code> - log of the GotCloud run
#:#<code>vcfs</code> - contains per chromosome directories with vcfs
#:#* important output is
#:#*# filtered.vcf.gz file: <code>vcfs/chr22/chr22.filtered.vcf.gz</code>
#:#*# summary information: <code>vcfs/chr22/chr22.filtered.sites.vcf.summary</code>
# Look at the filtered file.
#: <pre>zless -S output/vcfs/chr22/chr22.filtered.vcf.gz</pre>
#: Scroll down some: [[File:SnpVcfOutput.png|700px]]
## Check that GotCloud found the expected SNP at 22:36661906
##:<pre>tabix output/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 |head -1</pre>
#:[[File:SnpTabix.png|700px]]
# Look at the summary information
#:<pre>cat output/vcfs/chr22/chr22.filtered.sites.vcf.summary</pre>
#:[[File:SnpSummary.png|700px]]
#:*'''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.
