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VNtyper 2

Genotype MUC1 coding VNTRs for ADTKD-MUC1 diagnosis using short-read sequencing.

VNtyper 2 is a bioinformatics pipeline that detects frameshift mutations in the MUC1 Variable Number Tandem Repeat (VNTR) region, the genetic cause of Autosomal Dominant Tubulointerstitial Kidney Disease (ADTKD-MUC1). It combines mapping-free k-mer genotyping (Kestrel) with optional Profile-HMM validation (adVNTR) to deliver confidence-scored variant calls from BAM, CRAM, or FASTQ input.

  • Mapping-Free Genotyping

    Kestrel k-mer assembly avoids reference bias in repetitive VNTR regions, delivering empirically validated confidence scoring.

    How it works

  • Flexible Input

    Accepts BAM, CRAM, or paired-end FASTQ files with support for 8 reference assembly conventions across UCSC, NCBI RefSeq, and Ensembl.

    Input formats

  • Interactive Reports

    HTML reports with embedded IGV genome browser tracks, coverage metrics, and cohort-level summaries with optional pseudonymization.

    Output guide

Quick Install

# Recommended: install with all binary dependencies via Conda
git clone https://github.com/hassansaei/vntyper.git
cd vntyper
conda env create -f conda/environment_vntyper.yml
conda activate vntyper
pip install -e .

# Install reference assets
vntyper install-references -d reference   # from the repository root

# Run pipeline
vntyper pipeline --bam inputs/sample.bam -o results/sample/

Get started CLI Reference