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setup-borzoi_calico-remote-tool

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Set up, launch, validate, and troubleshoot the calico/borzoi variant-scoring (SAD/logSAD/D2/logD2) ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

skills/setup-borzoi_calico-remote-tool/SKILL.md

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# Set up calico's Borzoi variant scoring as a remote tool

> Validation status (2026-10-14): calico's own `borzoi_sad.py` at `5c93582` on
> `baskerville` at `544073b`, fold 0, reverse-complement ensemble, ran on the
> NVIDIA GB10 host (aarch64, 20 cores, 121.6 GiB unified, cc 12.1, driver
> 580.173.02) **on the CPU**, under kit mode `off`. The worker holds the model
> but **reimplements nothing numeric**: it imports stock's own
> `initialize_output_h5`, `write_snp_len` and `write_pct` out of `borzoi_sad`
> and calls `baskerville`'s own `snp_seq1`, `untransform_preds` and `seqnn`
> model in stock's order, then writes the same `sad.h5`. **This kit's `exact`
> mode is the first on this standard that actually runs on this host** — it
> ships no prebuilt host objects and its levers are Python data-path rewrites,
> not CUDA kernels — and it is byte-identical to stock across three pairs, all 16
> datasets; it is still set to `off` because no speed advantage could be
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