pcangsd
Link to section 'Introduction' of 'pcangsd' Introduction
PCAngsd is a program that estimates the covariance matrix and individual allele frequencies for low-depth next-generation sequencing (NGS) data in structured/heterogeneous populations using principal component analysis (PCA) to perform multiple population genetic analyses using genotype likelihoods.
For more information, please check its home page on Github.
Link to section 'Versions' of 'pcangsd' Versions
- 1.10
Link to section 'Commands' of 'pcangsd' Commands
- pcangsd
Link to section 'Module' of 'pcangsd' Module
You can load the modules by:
module load biocontainers
module load pcangsd
Link to section 'Example job' of 'pcangsd' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run PCAngsd on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=pcangsd
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers pcangsd
pcangsd -b pupfish.beagle.gz --inbreedSites \
--selection -o pup_pca2 --threads 12