samplot
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'samplot' Versions
- 1.3.0
Link to section 'Commands' of 'samplot' Commands
- samplot
Link to section 'Module' of 'samplot' Module
You can load the modules by:
module load biocontainers
module load samplot
Link to section 'Example job' of 'samplot' 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 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