lumpy-sv
Link to section 'Introduction' of 'lumpy-sv' Introduction
Lumpy-sv is a general probabilistic framework for structural variant discovery.
For more information, please check its website: https://biocontainers.pro/tools/lumpy-sv and its home page on Github.
Link to section 'Versions' of 'lumpy-sv' Versions
- 0.3.1
Link to section 'Commands' of 'lumpy-sv' Commands
- lumpy
- lumpyexpress
Link to section 'Module' of 'lumpy-sv' Module
You can load the modules by:
module load biocontainers
module load lumpy-sv
Link to section 'Example job' of 'lumpy-sv' 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 Lumpy-sv on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=lumpy-sv
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers lumpy-sv
lumpy -mw 4 -tt 0.0 -pe \
bam_file:AL87.discordant.sort.bam,histo_file:AL87.histo,mean:429,stdev:84,read_length:83,min_non_overlap:83,discordant_z:4,back_distance:1,weight:1,id:1,min_mapping_threshold:20 \
-sr bam_file:AL87.sr.sort.bam,back_distance:1,weight:1,id:2,min_mapping_threshold:20