HarmoniSV
A toolkit to harmonize and filter structural variations across methods and samples.
Last updated: 2026-07-25
Features
- Harmonize SVs discovered by different SV calling methods
- Filter high-confidence SVs with a random forest classifier
- Fast VCF manipulation, annotation, and conversion for SVs
Installation
Make sure you have Python 3.8+ and pip installed. Then, install the tool and its dependencies:
pip install HarmoniSV
Quick start
harmonisv
HarmoniSV: A toolkit to harmonize and filter structural variantions across methods and samples
Version: 0.1.1
Usage: harmonisv <command> [options]
Commands:
-- VCF manipulation
harmonize Harmonize SV VCFs across samples and SV calling methods
harmonize-header Harmonize VCF headers
sample2pop Convert single-sample VCF to multi-sample VCF
intersect Intersect SVs with genomic features
-- Analysis on SV callset
represent Select the representative SV from merged SVs
genotype Genotype SVs across SV genotyping methods
filter Random forest filter for SVs
concordance Calculate genotype concordance between two VCFs
Note:
1. All input VCFs MUST follow the VCF specification
2. Some commands assume unique SV IDs to index SVs
3. The input/output VCF format (i.e., vcf, vcf.gz, bcf) will be automatically detected. However, a
temporary uncompressed VCF file will be generated if the output is vcf.gz or bcf
For help on a specific command, run:
harmonisv <command> -h