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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's k-mer approach avoids reference bias in repetitive VNTR regions, with empirically validated confidence scoring.

    How it works

  • Flexible Input

    Accepts BAM, CRAM, or paired-end FASTQ files with support for hg19, hg38, GRCh37, and GRCh38 reference assemblies.

    Input formats

  • Interactive Reports

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

    Output guide

Quick Install

pip install git+https://github.com/hassansaei/VNtyper.git
vntyper install-references -d ./references
vntyper pipeline --bam sample.bam -o results/

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