HipSTR UI

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.

▶ Prefer not to install anything? Try https://hipstr.pages.dev

HipSTR-Web is the same workflow in a browser tab, with HipSTR compiled to WebAssembly. Your files never leave your machine there either — they are read locally, not uploaded — so it is a quick way to try HipSTR, or to read an existing VCF, without downloading an installer.

The desktop app remains the better fit for large or repeated runs: it uses the native binary and has no browser memory ceiling.

Quick Start

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.

How it works

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
   • HipSTR-generated genotype calls and locus-level coverage are shown directly in the interface, eliminating the need for manual parsing of VCF files
2. VCF interpretation & visualization
   • Load an existing HipSTR VCF
   • HipSTR-UI parses the file and provides interactive tables, allele plots, and exports

Exported Results (CSV / Excel)

HipSTR-UI allows users to export all displayed results as CSV or Excel files for downstream inspection, reporting, or archiving.

Exported tables include:

• Sample and locus identifiers
• Genotype calls as reported by HipSTR
• Base-pair differences relative to the reference allele
• Repeat period and reference allele information
• Locus-level sequencing depth (DP)
• Quality metrics and posterior probabilities (Q, PQ)
• Flags and annotations relevant for quality control

All exported values are directly extracted from the HipSTR VCF output and are provided for transparency and reproducibility. No additional filtering, normalization, or reinterpretation is applied during export.

Features

• 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)
• Qualitative allele distribution plots and quality metrics derived from HipSTR output
• Optional ISFG nomenclature adjustments for D19S433, D21S11, Penta D, and Penta E
• Log files to track execution and identify issues (e.g., ungenotyped loci)

Example Data (demodata folder)

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.

Citation

If you use HipSTR-UI, please cite:

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