Biowulf High Performance Computing at the NIH
SVPV on Biowulf

SVPV enables visualisation of predicted structural variant regions in paired-end whole genome sequencing alignments, and allows comparison of calls from differenct structural variant prediction algorithms. Statistics related to structural variants are presented in a form that allows users to visually identify false postive calls. Input is a set alignment files (SAM/BAM/CRAM format) along with a set of structural variant predictions on these alignments (VCF files). Output is a set of pdf files of structural variant regions. Please see the wiki for examples of SVPV plots of different structural variant categories.

SVPV supports VCF structural variant types deletion (DEL), duplication (DUP), copy number variation (CNV), inversion (INV), insertion (INS) and breakend ('BND'). Delly2-style translocations (TRA) are also supported.

References:

Documentation
Important Notes

SVPV creates and stores files in a subdirectory of your /home directory: ~/svpv_output.

Because this default output directory is limited to 8GB of space, it would be better to create a symlink to your /data directory. This is detailed in the interactive example, below.

SVPV has a GUI. Running the GUI requires an X-Windows connection.

SVPV -example -gui
SVPV_gui
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

[user@biowulf]$ sinteractive --cpus-per-task=1 --mem=10g --gres=lscratch:100
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 ~]$ mv ~/svpv_output /data/$USER/svpv_output
[user@cn3144 ~]$ ln -s /data/$USER/svpv_output ~/svpv_output
[user@cn3144 ~]$ SVPV -example
[user@cn3144 ~]$ SVPV -example -gui

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

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
module load SVPV
SVPV -vcf caller1_svs.vcf,caller2_svs.vcf \
  -samples sample1,sample2,sample3 \
  -aln s1.bam,s2.bam,s3.bam \
  -o /out/directory/ \
  -ref_vcf 1000_genomes_svs.vcf \
  -ref_gene hg38.refgene.txt \
  -max_len 100000 \
  -af <0.25 \
  -gts sample1:1/1,0/1;sample3:0/0 \
  -svtype DEL -exonic -ss 0 -se 1

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=1 --mem=10g --gres=lscratch:100 SVPV.sh