smoove
Link to section 'Introduction' of 'smoove' Introduction
Smoove simplifies and speeds calling and genotyping SVs for short reads.
For more information, please check its website: https://biocontainers.pro/tools/smoove and its home page on Github.
Link to section 'Versions' of 'smoove' Versions
- 0.2.7
Link to section 'Commands' of 'smoove' Commands
- smoove
Link to section 'Module' of 'smoove' Module
You can load the modules by:
module load biocontainers
module load smoove
Link to section 'Example job' of 'smoove' 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 Smoove on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=smoove
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers smoove
smoove call \
-x --name my-cohort \
--exclude hg38_blacklist.bed \
--fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa \
-p 24 \
--genotype input_bams/*.bam