Subnet Overview
Minos (SN107) is a merit-based competition for genomic variant calling on the Bittensor network. The system has two roles:Miners
Share their hyperparameter configuration for running variant-calling tools (GATK, DeepVariant, FreeBayes, or BCFtools). Compete on call accuracy.
Validators
Distribute tasks, benchmark results against truth sets, and assign scores that determine ALPHA rewards.
The Scoring Loop
Task Distribution
A validator selects a genomic region with a known truth set. It sends the miner aligned reads (BAM) and a reference genome for that region.
Variant Calling
The miner runs their chosen variant caller with their tuned hyperparameters. The output they share with the validator is their hyperparameter config.
Benchmarking
The validator uses the miner’s config to generate a VCF, then compares it against the truth set using standard metrics:
- Precision — what fraction of called variants are real
- Recall — what fraction of real variants were found
- F1-score — harmonic mean of precision and recall
Why Hyperparameters Matter
Every variant caller has dozens of tunable parameters that control sensitivity, specificity, and how the algorithm processes data. The default settings are general-purpose — they are not optimized for any specific benchmark. Miners who understand and tune these parameters gain a competitive edge:| Lever | Effect |
|---|---|
| Lower quality thresholds | More sensitive — finds more variants but risks false positives |
| Higher confidence thresholds | More precise — fewer false calls but may miss real variants |
| Adjusted priors | Control the model’s assumptions about variant frequency |
| Variant-type-specific parameters | Tune sensitivity per variant class |
| Contamination / PCR models | Model potential data artifacts |
Supported Tools at a Glance
| Tool | Approach | Docker Image |
|---|---|---|
| GATK | Local de novo assembly + Pair-HMM genotyping | broadinstitute/gatk:4.5.0.0 |
| DeepVariant | CNN image classification on pileup tensors | google/deepvariant:1.5.0 |
| FreeBayes | Bayesian haplotype evaluation with toggleable priors | staphb/freebayes:1.3.7 |
| BCFtools | Pileup-based genotype likelihoods + Bayesian caller | quay.io/biocontainers/bcftools:1.20 |