glnexus.rst

Glnexus

Introduction ~~~~~~~~ Glnexus: Scalable gVCF merging and joint variant calling for population sequencing projects.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/glnexus
Home page: https://github.com/dnanexus-rnd/GLnexus

Versions

• 1.4.1

Commands ~~~~~~~ - glnexus_cli

Module

You can load the modules by:

module load biocontainers
module load glnexus

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 glnexus on our clusters:

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

module --force purge
ml biocontainers glnexus

glnexus_cli --config DeepVariant \
    --bed ALDH2.bed \
    dv_1000G_ALDH2_gvcf/*.g.vcf.gz \
    > dv_1000G_ALDH2.bcf