View source for Bgc 2016

== Introduction ==
bgc  implements ''Bayesian estimation of genomic clines'' to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data.

== Installed versions ==
On environment ''hpc-env/6.4'':

'''bgc/1.03-intel-2018a'''

== Using bgc on the HPC cluster==
You need to switch to the new environment ''hpc-env/6.4'' before loading the ''bgc'' module:

 module load hpc-env/6.4
 module load bgc

=== Example job scripts ===

If you want to use bgc, it can be of use to create a job script. For example, it could look like this:

 ~
 #!/bin/bash
 
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 #SBATCH --mem=24G
 #SBATCH --time=0-18:00:00
 #SBATCH --output=slurm.%j.out
 #SBATCH --error=slurm.%j.err
 #SBATCH --mail-type=END,FAIL
 #SBATCH --mail-user=fynn.schwietzer1@uol.de
 
 
 ml hpc-env/6.4
 ml bgc/1.03-intel-2018a
 
 mkdir ~/bgc_test
 cp -r $EBROOTBGC/example/* ~/bgc_test
 cd ~/bgc_test
 bgc -a p0in.txt -b p1in.txt -h admixedin.txt -M map.txt -O 0 -x 50000 -n 25000 -p 1 -q 1 -N 1 -m 1 -D 0.5 -t 5 -E 0.0001 -d 1 -s 1 -I 0 -u 0.04
 
 done
 ~

In this example, the corresponding modules are being loaded, a test folder is getting created at your home directory (~/),  and some test files get copied in it.

At the end, the script starts to analyze the given data set.

This could take up to 18 hours, so this should just be seen as an example of a fitting job script.

== Documentation ==
If you want a short introduction to the available commands, you can use the help function after loading the module. Just type in: 
 bgc --help
The full documentation of AUGUSTUS can be found [https://sites.google.com/site/bgcsoftware/ here]. For further information you can find the manual [https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxiZ2Nzb2Z0d2FyZXxneDo0OWEwOWJjZGQzYmI2ZGY0 here]