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 here. For further information you can find the manual here