GTSNPSpring2012

=**Genotype and SNP-calling from Next-Generation Sequencing data**=

April 2, 2012
The step-by-step instructions for classroom exercises can be found at this [|workshop site]. Below are the instructions for downloading data to get an early start.

**Note:** This has only been tested on Linux and OSX.
This workshop will guide you through some basic exercises using the program called //**'dirty'**// and R //http://www.r-project.org///. Please go to R Project web site to download the program. The data needed for this tutorial is in two tar.gz files, that you can download here //[]// and here //[]//.

CONTENTS

 * //**dirty_src/:**// This contains the sources used for building the program
 * **//precompiled/://** This contains precompiled binary files for X32 and X64. For UNIX we have also compiled the programs staticly in case you have problems. For OSX we have only compiled it for 32bit.
 * //**LCT.data/:**// datafiles containing data surrounding the LCT region, for 25 danes
 * **//exampleOutput/://** This is output of the programs generated if you follow this website. Use this if you for some reason have problems running the program
 * **//simulated.data/://** This contains simulated data ready to be used for PCA analysis.

INSTALLATION
You unpack the .tar.gz with //tar xfvz workshop.tar.gz// //tar xfvz simulated.data.tar.gz// then move everything is a single folder //cp -R simulated.data rasmus.workshop// //rm -r simulated.data// This creates the folder called rasmus.workshop. Move into this folder. //cd rasmus.workshop/// We will use 2 programs, 'dirty' and 'optimSFS', and several R scripts. We can use the precompiled binaries or we can build the programs our selves. In either case we will need to have these program in the root of the unpacked folder.

**1) Using precompiled binaries:** You can simply copy or make links to the precompiled files in the appropiate subdirectory in the precompiled folder:
//ln -fs precompiled/linux/optimSFS.x32 optimSFS// //ln -fs precompiled/linux/dirty.x32 dirty// The above is for a Linux 32bit platform, which should also work for linux 64bit platform. For OSX the commands would be //ln -fs precompiled/osx/optimSFS.x32 optimSFS// //ln -fs precompiled/osx/dirty.x32 dirty// If there are problems due to missing shared object files, you can try the files in the '//precompiled/linux.static///' directory, which 'should' be standalone without any dependencies.

**2) Building source files**
If the precompiled won't run you can compile it for youself. This will be done for you, along with creating appropiate symlinks to the correct files with: //./install.sh// If for some reason this won't work. Then try first: //cd dirty_src/;make clean ;cd misc;make clean ;cd ../samtools-0.1.17/;make clean;cd ../../;// And then try recompiling //cd dirty_src/misc ;make ; cd ../samtools-0.1.17/;make ;cd ..;make;cd ..;// And now we make symlinks to the executables //ln -fs dirty_src/misc/optimSFS.gcc optimSFS// //ln -fs dirty_src/dirty/dirty.g++ dirty//

If everything went fine, when you type //./dirty// or //./optimSFS// you should get some info messages.

If you have problems or questions on downloading data or installing programs, please let me know matteo.fumagalli@berkeley.edu. Any way, we are gonna guide the installation step by step during the workshop.