GotCloud: Amazon Demo

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

See Amazon Single Node for instructions on starting a node and getting a terminal running.

• For the demo, we recommend using a c3.2xlarge instance.

Running the Demo on Already Running Node

Examine the Setup

1. After logging into the Amazon node as the ubuntu user, you should by default be in the ubuntu home directory: /home/ubuntu
   1. You can check this by doing:

      pwd

      • This should output: /home/ubuntu
   2. Take a look at the contents of the ubuntu user home directory

      ls

      • This should output be 2 directories, example and gotcloud
        • The example directory contains the files for this demo
        • The gotcloud directory contains the gotcloud programs and pre-compiled source

   

2. Look at the example input files:

   ls example

   

   1. bam.list contains the list of BAM files per sample
   2. bams is a subdirectory containing the BAM files for this demo
   3. test.bed 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

      

   4. test.conf contains the settings we want GotCloud to use for this run

      

      • For the demo, we want to tell GotCloud:
        1. The list of bams to use: BAM_LIST = example/bam.list
        2. The region to process rather than the whole genome: UNIFORM_TARGET_BED = example/test.bed
        3. The chromosomes to process. The default chromosomes are 1-22 & X, but we only want to process chromosome 22: CHRS = 22

Run GotCloud SnpCall

Now that we have examined the instance files, run GotCloud snpcall

1. gotcloud snpcall --conf example/test.conf --outdir output --numjobs 8

   • 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

   

   • 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.

2. When complete, GotCloud snpcall will indicate success/failure