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.

Versions

• 0.3.1

Commands

• lumpy

• lumpyexpress

Module

You can load the modules by:

module load biocontainers
module load lumpy-sv

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 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