HipSTR-UI is an easy-to-use graphical interface for the HipSTR tool

Comes with a pre-built HipSTR binary for Windows, macOS, and Linux. It was designed for forensic analysts, students, and researchers who need a simple way to run HipSTR or interpret its results without command-line skills

Built with Electron and Chakra UI.

1. Download the installer for your system from the latest release for your operating system from the Releases page

• Windows: hipstr-ui.Setup.exe
• macOS Apple Silicon (M1/M2/M3): hipstr-ui-darwin-arm64.zip
• Ubuntu/Debian: hipstr-ui_amd64.deb

Do not download “Source code (zip/tar.gz)” unless you want to build from source.

HipSTR-UI operates in two complementary modes:

1. Full pipeline execution
   • Input: BAM/CRAM files, BED file (STR regions), and reference FASTA
   • HipSTR-UI runs HipSTR locally, producing:
     • a VCF file with genotyping results
     • a log file with detailed execution steps
   • Final genotypes and coverage are shown directly in the interface no manual calculations needed
2. VCF interpretation & visualization
   • Load an existing HipSTR VCF
   • HipSTR-UI parses the file and provides interactive tables, allele plots, and exports

• Runs fully offline all data stays on your computer
• Two modes: Run HipSTR pipeline or Visualize existing VCFs
• Interactive results table with filtering and export (CSV/Excel)
• Allele coverage plots and quality metrics
• Optional ISFG nomenclature adjustments for D19S433, D21S11, Penta D, and Penta E
• Log files to track execution and identify issues (e.g., ungenotyped loci)

The repository includes a demodata folder containing example datasets to help users test the interface and validate results.

Contents:

• samples/ — CRAM and CRAI files from 1000 Genomes Project (publicly available)
• results/ — example outputs generated by HipSTR (VCF and log files)
• regions.bed — genomic coordinates of STR loci used for capture
• README_demodata.txt — detailed explanation of each file and how to use them

To run the example pipeline, download the reference FASTA file (link provided in README_demodata.txt) and place it in the same folder as the demo files before execution.

If you use HipSTR-UI, please cite:

• HipSTR-UI (manuscript in prep)
• Willems T, et al. HipSTR: Variant calling for STRs. Nat Methods 2017