Documentation • McVicker Lab • Original WASP

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Installation

Recommended: Bioconda

mamba install -c conda-forge -c bioconda wasp2

Installs WASP2 and all dependencies (samtools, bcftools, bedtools, htslib) automatically. Available for Linux (x86_64, aarch64) and macOS (Intel, Apple Silicon). Requires miniforge.

Via PyPI

pip install wasp2

Pre-built wheels for Linux (x86_64, aarch64) and macOS (Intel, Apple Silicon) with Python 3.10-3.13. The Rust extension and htslib are bundled in the wheel. Requires samtools, bcftools, and bedtools installed separately.

For development

git clone https://github.com/mcvickerlab/WASP2.git
cd WASP2
pixi install        # resolves all dependencies including Rust toolchain
pixi run verify     # build + test

Via Docker

docker pull ghcr.io/mcvickerlab/wasp2:1.4.0
docker run --rm -v $PWD:/data ghcr.io/mcvickerlab/wasp2:1.4.0 wasp2-count --help

Multi-platform image (linux/amd64 + linux/arm64) with all dependencies included.

Via Singularity/Apptainer (HPC)

singularity pull wasp2.sif docker://ghcr.io/mcvickerlab/wasp2:1.4.0
singularity exec wasp2.sif wasp2-count --help

Reproducible Environment (conda-lock)

For fully pinned, reproducible installs (HPC clusters, CI, shared lab environments):

# Recommended: mamba (fastest)
mamba create -n WASP2 --file conda-lock.yml

# Or with conda
conda-lock install -n WASP2 conda-lock.yml

conda-lock.yml pins every package to exact versions with checksums for linux-64 and osx-64. To regenerate after updating environment.lock.yml:

conda-lock lock -f environment.lock.yml --lockfile conda-lock.yml

See the documentation for detailed install options and development setup.

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).