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SVPV

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.

There are multiple versions of SVPV available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail SVPV

To select a module, type

module load SVPV/[ver]

where [ver] is the version of choice.

Environment variables set:

Interactive job on Biowulf

An interactive session can be started like this:

sinteractive --cpus-per-task=1 --mem=10g --gres=lscratch:100

Once the interactive session has started, a simple example can be run:

SVPV -example

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, like so:

mv ~/svpv_output /data/$USER/svpv_output
ln -s /data/$USER/svpv_output ~/svpv_output

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

SVPV -example -gui
SVPV_gui
Batch job on Biowulf

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
Documentation