samplot is a command line tool for rapid, multi-sample structural variant visualization. samplot takes SV coordinates and bam files and produces high-quality images that highlight any alignment and depth signals that substantiate the SV.

References:

• https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02380-5

• https://github.com/ryanlayer/samplot

• Module Name: samplot (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --gres=lscratch:10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load samplot

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3144 ~]$ cp -r $SAMPLOT_TEST_DATA .

[user@cn3144 ~]$ samplot plot \
    -n NA12878 NA12889 NA12890 \
    -b TEST_DATA/data/NA12878_restricted.bam \
      TEST_DATA/data/NA12889_restricted.bam \
      TEST_DATA/data/NA12890_restricted.bam \
    -o 4_115928726_115931880.png \
    -c chr4 \
    -s 115928726 \
    -e 115931880 \
    -t DEL
[W::hts_idx_load3] The index file is older than the data file: TEST_DATA/data/NA12878_restricted.bam.bai
[W::hts_idx_load3] The index file is older than the data file: TEST_DATA/data/NA12878_restricted.bam.ba

[user@cn3144 ~]$ ls 4_115928726_115931880.png
4_115928726_115931880.png

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load samplot
cd /lscratch/$SLURM_JOB_ID
cp -r /usr/local/apps/${APP}/TEST_DATA .
samplot plot \
    -n NA12878 NA12889 NA12890 \
    -b TEST_DATA/data/NA12878_restricted.bam \
      TEST_DATA/data/NA12889_restricted.bam \
      TEST_DATA/data/NA12890_restricted.bam \
    -o 4_115928726_115931880.png \
    -c chr4 \
    -s 115928726 \
    -e 115931880 \
    -t DEL

Submit this job using the Slurm sbatch command.

sbatch batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; samplot plot -n NAME1 -b BAM1 -o IMAGE1.png
cd dir2; samplot plot -n NAME2 -b BAM2 -o IMAGE2.png
cd dir3; samplot plot -n NAME3 -b BAM3 -o IMAGE3.png

Submit this job using the swarm command.

swarm -f job.swarm --module samplot