AnnotSV is a robust open-source software package and web-based platform designed for the annotation and prioritization of structural variants (SVs) in the human genome. Because the native installation process can be somewhat involved, I provide a Singularity container that bundles AnnotSV for straightforward, ready-to-use deployment. For details on installing Singularity, please refer to the guide “Singularity Installation and Usage Tutorial: A Containerization Guide for High-Performance Computing Environments”.

AnnotSV 3.5.3 （2025.10.31）：
Singularity Repository
Huggingface Repository

This Singularity container bundles AnnotSV to enable convenient deployment in Linux-based environments.

Original AnnotSV project: AnnotSV GitHub
Original project license: GPL-3.0
This container inherits the GPL-3.0 license from the upstream project.

The AnnotSV source code and installation within the container are located at:
/opt/software/AnnotSV_3.5.3/AnnotSV/

During the container build process, various warnings, errors, or temporary log files may have been generated and left behind. The author does not take responsibility for these residual files, as it is not feasible to track every intermediate change or artifact created during installation. If users wish to study the AnnotSV installation process based on these logs, they are encouraged to review and test them carefully.

This image is actively used in long-term workflows. Any issues discovered will be addressed promptly, and updated container versions will be uploaded to the repository.

The distribution of this codebase and the packaged software complies with the terms of the GPL-3.0 license.

Bash
#!/usr/bin/env bash
set -e

# Create the installation directory

echo "===== download annotation files ====="

# Human
curl -C - -LO "https://www.lbgi.fr/~geoffroy/Annotations/Annotations_Human_3.5.tar.gz"
# Mouse
curl -C - -LO "https://www.lbgi.fr/~geoffroy/Annotations/Annotations_Mouse_3.4.2.tar.gz"
# Exomiser phenotype
curl -C - -LO "https://data.monarchinitiative.org/exomiser/data/2406_phenotype.zip"
# Exomiser JAR
curl -C - -LO "https://github.com/exomiser/Exomiser/releases/download/14.1.0/exomiser-rest-prioritiser-14.1.0.jar"

echo ""
echo "===== Download complete, starting extraction ====="
mkdir -p ./AnnotSV_3.5.3_anno

# Extract Human annotations
tar -xf Annotations_Human_3.5.tar.gz -C ./AnnotSV_3.5.3_anno
# Extract Mouse annotations
tar -xf Annotations_Mouse_3.4.2.tar.gz -C ./AnnotSV_3.5.3_anno
# Extract Exomiser phenotype data
mkdir -p ./AnnotSV_3.5.3_anno/Annotations_Exomiser/2406
unzip -o 2406_phenotype.zip -d ./AnnotSV_3.5.3_anno/Annotations_Exomiser/2406
# Place the Exomiser JAR
mkdir -p ./AnnotSV_3.5.3_anno/jar
mv exomiser-rest-prioritiser-14.1.0.jar ./AnnotSV_3.5.3_anno/jar

# Clean compressed archives
# rm -f Annotations_Human_3.5.tar.gz
# rm -f Annotations_Mouse_3.4.2.tar.gz
# rm -f 2406_phenotype.zip

echo ""
echo "===== All data installation complete ====="
# echo "Install directory: $(pwd)"

This image is built with Singularity (version 3.5.3) and therefore requires a Singularity environment to run.

Bash
singularity exec AnnotSV_3.5.3.sif \
    AnnotSV \
        -SVinputFile 'Path of your VCF or BED input file with SV coordinates' \
        -outputFile 'Output path and file name' \
        -genomeBuild 'GRCh38 or GRCh37 or CHM13 or or mm9 or mm10' \
        -annotationsDir 'Path of the annotations directory' \
        -svtBEDcol 4 -vcf 0 \
        -PhenoGeniusCli True \
        -hpo "HP:0011003,HP:0030329" \
        -prioritiserParams human,ppi \
        -txFile 'Path of a file containing a list of preferred genes transcripts to be used in priority during the annotation (Preferred genes transcripts names should be tab or space separated)'