Lancet2 is an accurate variant caller (SNVs and InDels) for short read sequencing data, supporting flexible single-sample through multi-sample analysis via localized colored de Bruijn graph assembly.

In addition to variant calling accuracy and improved somatic filtering, Lancet2 has significant runtime performance improvements compared to Lancet1 (up to ~10× speedup and ~50% less peak memory usage).

Lancet2 packages with Cloud I/O support (s3://, gs://, http(s)://, ftp(s)://) are published to prefix.dev/channels/lancet2. Install using your preferred package manager:

Development builds are published on every push to main. Stable releases are published with every tagged release. To install a specific stable release, pin the version:

# Stable releases: clean numbers (e.g., 2.9.0)
# Dev builds: version_branch_hash (e.g., 2.9.0_main_441d081927)
# Find versions at https://prefix.dev/channels/lancet2/packages/lancet2
export LANCET_VERSION="2.9.0"
pixi global install --channel https://prefix.dev/channels/lancet2 "lancet2==${LANCET_VERSION}"

Pre-built packages are available for linux-64 (x86-64-v3, Haswell 2013+) and macOS ARM64 (Apple Silicon M1+).

Pre-built Docker images are available from Google Artifact Registry. A CPU with x86-64-v3 support (Haswell 2013+: AVX2, BMI2, FMA) is required. Docker tags follow the same convention: stable releases use clean version numbers (X.Y.Z), dev builds include branch and commit hash (X.Y.Z_main_<hash>).

docker pull us-central1-docker.pkg.dev/nygc-app-c-148c/lancet-public/lancet:X.Y.Z

See the Installation Guide for build-from-source instructions, including static and Cloud I/O build variants.

Tumor-normal somatic calling — the primary supported workflow. In the VCF, --tumor maps to CASE and --normal maps to CTRL (why?):

Lancet2 pipeline \
    --normal /path/to/normal.bam \
    --tumor /path/to/tumor.bam \
    --reference /path/to/reference.fasta \
    --region "chr22" --num-threads $(nproc) \
    --out-vcfgz /path/to/output.vcf.gz

Lancet2 also supports single-sample (germline/mosaic) and multi-sample modes. See the full documentation for details.

See full documentation for VCF output format, CLI reference, and pipeline architecture.

See publications associated with Lancet.

Lancet2 is distributed under the BSD 3-Clause License.

Informatics Technology for Cancer Research (ITCR) under the NCI U01 award 1U01CA253405-01A1.