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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 == |
− | === Examine the Setup ===
| + | {{GotCloud: Amazon Demo Setup}} |
− | #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>
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| === 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> |
− | #: Scroll down some: [[File::SnpVcfOutput.png|700px]] | + | #: 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> |
− | #:[[File::SnpTabix.png|700px]] | + | #:[[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 === |