glnexus
Link to section 'Introduction' of 'glnexus' Introduction
Glnexus: Scalable gVCF merging and joint variant calling for population sequencing projects.
BioContainers: https://biocontainers.pro/tools/glnexus
Home page: https://github.com/dnanexus-rnd/GLnexus
Link to section 'Versions' of 'glnexus' Versions
- 1.4.1
Link to section 'Commands' of 'glnexus' Commands
- glnexus_cli
Link to section 'Module' of 'glnexus' Module
You can load the modules by:
module load biocontainers
module load glnexus
Link to section 'Example job' of 'glnexus' 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 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