From Genome Analysis Wiki
Jump to navigationJump to search
2,247 bytes added
, 09:50, 17 October 2014
Line 1: |
Line 1: |
| + | == 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]] |
| | | |
| == Starting up a Node == | | == Starting up a Node == |
| See [[Amazon Single Node]] for instructions on starting a node and getting a terminal running. | | 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 == | | == Running the Demo on Already Running Node == |
| + | |
| + | #After logging into the Amazon node as the ubuntu user, you should by default be in the ubuntu home directory: <code>/home/ubuntu</code> |
| + | ## You can check this by doing: |
| + | ##:<pre>pwd</pre> |
| + | ##* This should output: <code>/home/ubuntu</code> |
| + | ## Take a look at the contents of the ubuntu user home directory |
| + | ##: <pre>ls</pre> |
| + | ##* This should output be 2 directories, <code>example<code> and <code>gotcloud</code> |
| + | ##** The <code>example</code> directory contains the files for this demo |
| + | ##** The <code>gotcloud</code> directory contains the gotcloud programs and pre-compiled source |
| + | #:[[File:DemoHome.png|400px]] |
| + | # Look at the example input files: |
| + | #:<pre>ls example</pre> |
| + | #:[[File:ExampleFiles.png|400px]] |
| + | #:# <code>bam.list</code> contains the list of BAM files per sample |
| + | #:# <code>bams</code> is a subdirectory containing the BAM files for this demo |
| + | #:# <code>test.bed</code> contains the region we want to process in this demo |
| + | #:#* 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 |
| + | #:#:[[File:BedContents.png|400px]] |
| + | #:# <code>test.conf</code> contains the settings we want GotCloud to use for this run |
| + | #:#:[[File:ConfContents.png|400px]] |
| + | #:#:* For the demo, we want to tell GotCloud: |
| + | #:#:*# The list of bams to use: <code>BAM_LIST = example/bam.list</code> |
| + | #:#:*# The region to process rather than the whole genome: <code>UNIFORM_TARGET_BED = example/test.bed</code> |
| + | #:#:*# The chromosomes to process. The default chromosomes are 1-22 & X, but we only want to process chromosome 22: <code>CHRS = 22</code> |