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.

Versions

• 1.10

Commands

• pcangsd

Module

You can load the modules by:

module load biocontainers
module load pcangsd

Example job

Warning

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