TAGster 1.0

Requirements:

The free software R (http://cran.us.r-project.org/) needs to be installed for TAGster to create Figures. 

TAGster assumes that the directory path to R has been set and that R can be run when typed "R" in command line. 

If the directory path to R has not been set, users can either set the parameter value for "-Rcommand" in the parameter file "params.txt" to provide the directory path to R or add the directory path to R into the system default path by doing the following:

For MS Windows XP:
.	Right-click My Computer, and then click Properties.
.	Click the Advanced tab.
.	Click Environment variables.
.	Navigate system variables to "Path", then click Edit
.	Add the R directory to the end of variable value, such as ";C:\Program Files\R\R-2.5.1\bin" NOTE: Do not forget to put a ";" to separate R path with the preceding path value and specify the correct version of R (here shown as 2.5.1). 

To show system default path:
.	click start
.	click run
.	type cmd, then click ok to open command window. 
.	type command "path" to show the default path.


For Linux

.	Type "cd"  to go to home directory
.	Type "vi  .bash_profile" to open the system file ".bash_profile"
.	Add R path to the end of the variable value for PATH, such as  ":/usr/lib64/R/bin." Do not forget to put a ":" to separate R path with the preceding path value.
To show system default path:
.	Type "echo $PATH"




How to run the software:

On the command line, cd to the directory of TAGster and type 

TAGster

or double click the file TAGster in windows. On the command line type

TAGster > output_file

to output the standard screen output to the file output_file

If one wants to select tag SNPs using genotype files in HapMap format or Prettybase format, the user must first run the conversion utility to convert genotype files into the correct format for TAGster. 

To run conversion utility, type or double click

              fconvert




The content of software TAGster is as following:

.	2 executable files TAGster and fconvert under root directory of tagster;
.	4 example genotype files (African, asian, ceu and hisp) under default input directory indir;
.	1 example file if the user wishes to require inclusion of certain SNPs as tag SNPs (include.txt) under default input directory indir;
.	1 example file if the user wishes to require exclusion of certain SNPs from tag SNPs (exclude.txt) under default input directory indir;
.	1 example file of a non-synonymous SNP list (nssnp) under default input directory indir;
.	1 example file of a user-specified SNP design score (score.csv,) under default input directory indir; these are purely simulated values from 0 to 1, and are not actual design scores for corresponding SNPs.
.	1 perl file (snprspos.pl) to replace Seattle SNP id with rs number under default input directory indir;
.	1 example file of a list rs number and Seattle SNP correspondence (rs_example.csv) under default input directory indir;
.	6 example genotype files in HapMap format and 1 list file under default HapMap file directory indir/hapmap;
.	2 example genotype files in Prettybase format, 1 genotype list file and 1 individual list file under default Prettybase file directory indir/prettybase;
.	1 default output directory outdir.


