Samplot

Introduction

Samplot is a command line tool for rapid, multi-sample structural variant visualization.

For more information, please check its website: https://biocontainers.pro/tools/samplot and its home page on Github.

Versions

1.3.0

Commands

samplot

Module

You can load the modules by:

module load biocontainers
module load samplot

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 Samplot on our clusters:

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

module --force purge
ml biocontainers samplot

samplot plot \
-n NA12878 NA12889 NA12890 \
-b samplot/test/data/NA12878_restricted.bam \
  samplot/test/data/NA12889_restricted.bam \
  samplot/test/data/NA12890_restricted.bam \
-o 4_115928726_115931880.png \
-c chr4 \
-s 115928726 \
-e 115931880 \
-t DEL