wasp2 1.4.0

Allele-specific analysis of next-generation sequencing data with high-performance multi-format variant support (VCF/cyvcf2/PGEN)

Documentation • McVicker Lab • Original WASP

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Installation

Recommended: pixi (one command, all dependencies)

# Install pixi if you don't have it
curl -fsSL https://pixi.sh/install.sh | bash

# Clone and install
git clone https://github.com/mcvickerlab/WASP2.git
cd WASP2
pixi install

This resolves Python, Rust, samtools, bcftools, bedtools, and htslib automatically. No system packages required.

Via PyPI (pre-built wheels)

pip install wasp2

Pre-built wheels are available for Linux (x86_64, aarch64) and macOS (Intel, Apple Silicon) with Python 3.10-3.13. The Rust extension and htslib are bundled — no additional dependencies required. You still need samtools, bcftools, and bedtools on your PATH.

See the documentation for mamba/conda, Docker, and Singularity install options.

Quick Start

WASP2 has three steps that run in order:

Step 1: Remap reads to correct mapping bias

wasp2-map make-reads input.bam variants.vcf.gz -s sample1 -o remap_dir/
# Realign the swapped-allele reads with your aligner, then:
wasp2-map filter-remapped remapped.bam -j remap_dir/sample1_wasp_data_files.json -o filtered.bam

Step 2: Count alleles at heterozygous SNPs

wasp2-count count-variants filtered.bam variants.vcf.gz -s sample1

Step 3: Test for allelic imbalance

wasp2-analyze find-imbalance counts.tsv -o results.tsv

See the documentation for detailed usage, single-cell workflows, and supported variant formats (VCF, BCF, PGEN).

Authors

• Aaron Ho — Creator of WASP2
• Jeff Jaureguy — Developer and maintainer
• McVicker Lab, Salk Institute

Citation

If you use WASP2 in your research, please cite our paper (coming soon).