BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model.
| Info |
|---|
This package is built using SPACK and optimized for AVX, AVX2 and AVX512 CPUs. To use the optimized version, you need to add source /etc/profile.d/zlmod.sh to your submit script before loading any modules. By default, the AVX2 optimized version (head node is Haswell CPU) is in your path. The AVX2 optimized version will run on Skylake (enge, im2080, chem, health) and Cascade Lake (hawkcpu, hawkmem, hawkgpu, infolab) CPUs but not on Ivybridge (debug) CPUs. |
| Version | module name |
|---|
| 2.1 | bayescan/2.1 |
| Code Block |
|---|
| language | bash |
|---|
| title | Example Script, available at /share/Apps/examples/bayescan |
|---|
| collapse | true |
|---|
|
#!/bin/bash
#SBATCH -p lts
#SBATCH -t 60
#SBATCH -n 20
#SBATCH -N 1
#BayeScan can only be run on a single node
# Load BayeScan module
module load bayesan/2.1
# Set number of OpenMP Threads
export OMP_NUM_THREADS=${SLURM_NTASKS}
cd ${SLURM_SUBMIT_DIR}
bayescan_2.1 test_band_intensity_AFLP.txt
# Want to use different number of threads, say 10
bayescan_2.1 test_binary_AFLP.txt -threads 10
# Use SNP genotypes matrix (See manual for more details)
bayescan_2.1 test_genotype_SNP.txt -snp
# Optional input file (discarded.txt) containing list of loci to discard
bayescan_2.1 test_msats.txt -d discarded
bayescan_2.1 test_SNPs.txt -d discarded.txt -snp -threads 10 |
...