Ngsld

Introduction

ngsLD is a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype’s assignation into account. It does so by avoiding genotype calling and using genotype likelihoods or posterior probabilities.

For more information, please check:

Home page: https://github.com/fgvieira/ngsLD

Versions

• 1.1.1

Commands

• ngsLD

Module

You can load the modules by:

module load biocontainers
module load ngsld

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 ngsld on our clusters:

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

module --force purge
ml biocontainers ngsld