Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

References:

• Blow J., Doe J. A ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data Genome Medicine. 2021;13:32

• clinsv Main Site

This application requires a graphical connection using NX

• Module Name: clinsv (see the modules page for more information)
• Environment variables set
  • clinsv_HOME
• Example files in /usr/local/apps/clinsv/sample
• Reference data in /usr/local/apps/clinsv/ref_hg38/clinsv/refdata-b38

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
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 clinsv

[user@cn3144 ~]$  

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

Most jobs should be run as batch jobs.

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

#!/bin/bash
set -e
module load clinsv
cd /some/place/with/bamfile/abc.bam
mkdir -p test_run
refdata_path=/usr/local/apps/clinsv/ref_hg38/clinsv/refdata-b38
input_path=$PWD
project_folder=$PWD/test_run

singularity run --bind $refdata_path:/app/ref-data/refdata-b38 \
        --bind $project_folder:/app/project_folder \
        --bind $input_path:/app/input \
        /usr/local/apps/clinsv/1.1/libexec/1.1.sif \
        /app/clinsv/bin/clinsv \
        -r all \
        -p /app/project_folder/ \
        -i "/app/input/abc.bam" \
        -ref /app/ref-data/refdata-b38

Submit this job using the Slurm sbatch command.

sbatch -c 16 --mem=80g clinsv.sh

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

clinsv < clinsv.in > clinsv.out
clinsv < clinsv.in > clinsv.out
clinsv < clinsv.in > clinsv.out
clinsv < clinsv.in > clinsv.out

Submit this job using the swarm command.

swarm -f clinsv.swarm [-g #] [-t #] --module clinsv