Dsuite

Introduction

Dsuite is a fast C++ implementation, allowing genome scale calculations of the D and f4-ratio statistics across all combinations of tens or hundreds of populations or species directly from a variant call format (VCF) file.

For more information, please check its home page on Github.

Versions

• 0.4.r43

• 0.5.r44

Commands

• Dsuite

• dtools.py

• DtriosParallel

Module

You can load the modules by:

module load biocontainers
module load dsuite

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 Dsuite on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=dsuite
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers dsuite

Dsuite Dtrios -c -n no_geneflow -t simulated_tree_no_geneflow.nwk chr1_no_geneflow.vcf.gz species_sets.txt