Reference Assemblies¶

VNtyper 2 supports multiple reference genome assemblies with automatic chromosome naming detection.

Supported Assemblies¶

MUC1 VNTR Region Coordinates¶

All assemblies within the same coordinate system use identical coordinates:

The BAM extraction region is wider to capture flanking reads. The VNTR region is the precise target used for coverage calculation.

Auto-Detection from BAM Headers¶

When processing BAM or CRAM input, VNtyper 2 detects the chromosome naming convention from the file header and constructs the correct region string automatically. For example, a BAM aligned to an Ensembl reference (chromosomes named 1, 2, ...) with --reference-assembly hg19 will produce the region 1:155158000-155163000.

When to Use --reference-assembly¶

vntyper pipeline --bam sample.bam -o results/ --reference-assembly hg38

Specify this option when:

• Your BAM is aligned to hg38/GRCh38 (VNtyper 2 defaults to hg19)
• You want to explicitly select the chromosome naming convention (e.g., hg19_ensembl for Ensembl-style names)
• You are using FASTQ input (no BAM header available for auto-detection)

Installing References¶

Before running the pipeline, install reference files:

vntyper install-references -d /path/to/references --threads 4

To install specific assemblies or aligners:

vntyper install-references -d /path/to/references \
    --references hg19 hg38 \
    --aligners bwa bwa-mem2