merge-cli 3.7

MERGE variant pathogenicity prediction CLI with precomputed VCF cache and local/remote model integrations

merge-cli 3.7

MERGE variant pathogenicity prediction CLI.

Highlights

• Remote and local prediction modes.
• Local precomputed VCF cache lookup for hg38/hg19 coding and splicing variants.
• Local/remote model switches for AlphaGenome, HyenaDNA, NT, Evo2, Enformer, GENERATOR, GENERATOR-v2, and NT-v2.
• Bundled MERGE ensemble model files.

Quick Start

pip install merge-cli
merge --help
merge predict --chrom chr1 --pos 69428 --ref T --alt G --genome hg38

Precomputed VCF Cache

merge precomputed configure --data-dir /path/to/precomputed
merge precomputed status
merge precomputed download --genome all --variant-type all

Expected files include coding_merged.vcf.gz, splicing_merged.vcf.gz, their hg19 counterparts, and .tbi indices.

GENERATOR / GENERATOR-v2 / NT-v2

These models use one external service by default at http://127.0.0.1:18004.

merge generator-ntv2 configure --url http://127.0.0.1:18004
merge generator-ntv2 status
merge predict --chrom chr1 --pos 69428 --ref T --alt G --generator --generator-v2 --nt-v2

Local mode uses the same service URL:

merge predict --local --chrom chr1 --pos 69428 --ref T --alt G --ensemble-type coding --generator --generator-v2 --nt-v2

Service contract:

• GET /health
• POST /predict with chrom, pos, ref, alt, genome_version, models
• POST /batch_predict with variants, models

Model keys: generator, generator_v2, nt_v2.

Enformer

merge enformer configure --url http://localhost:5004
merge enformer status

If local services are unavailable, errors are reported under prediction.errors and the CLI continues returning available results.