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### SpliceAI Variant Scoring (`spliceai-score`) Scores genetic variants (chromosome / 1-based position / ref / alt) for splice-altering effects, returning per-gene delta scores and delta positions for acceptor and donor gain/loss. Requires a reference genome FASTA and a gene annotation (the bundled `grch37`/`grch38`, or a custom file). #### API Reference

Source Variants to score. A single variant is auto-wrapped into a list. Chromosome identifier, matching the reference FASTA and annotation (e.g. `'chr1'` or `'1'` — be consistent across all three). Variant position, 1-based (VCF convention). Reference allele, e.g. `'A'` or `'AC'` (DNA bases A/C/G/T/N). Alternate allele, e.g. `'G'` or `'GTT'` (DNA bases A/C/G/T/N).

Source Path (or AssetRef) to the reference genome FASTA. Required at call time — SpliceAI extracts the wild-type sequence around each variant from this genome. `None` raises a `MissingAssetError` so un-provisioned hosts skip cleanly. Gene annotation source: `'grch37'` or `'grch38'` (GENCODE files bundled with SpliceAI) or a path to a custom tab-separated annotation file. Maximum distance (bp) between the variant and a gained/lost splice site to report (the SpliceAI `-D` flag). Mask scores for annotated acceptor/donor gain and unannotated acceptor/donor loss (the SpliceAI `-M` flag). Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run inference on. SpliceAI (TensorFlow) auto-falls-back to CPU when no GPU is visible. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Per-variant scores, 1:1 with the input variants and in the same order. Variant chromosome. Variant position (1-based). Reference allele. Alternate allele. One record per gene the variant overlaps (empty if it overlaps no annotated gene). Per-variant scalar metric (max delta score). **Metrics** (one set per `results` item) | Metric | Type | Range | Availability | | ----------------- | ----- | ---------- | --------------------------------------------------------- | | `max_delta_score` | float | 0.0 to 1.0 | present for scored variants overlapping an annotated gene |

#### Applications Use this to triage candidate variants from a sequencing study for splicing impact, to annotate a VCF with SpliceAI predictions, or to prioritize variants of uncertain significance where a coding effect is absent but a splicing effect is plausible. The `max_delta_score` metric supports threshold-based filtering at the recommended 0.2 / 0.5 / 0.8 cutoffs. #### Usage Tips * **`reference_fasta` is required and `position` is 1-based.** SpliceAI extracts the wild-type window around each variant from the genome you supply, so the FASTA, the annotation, and each variant's `chromosome` must use consistent identifiers. Note this is the opposite of `AlphaGenome`, whose coordinates are 0-based. * **`annotation` selects the gene model.** `grch37` and `grch38` load the GENCODE files bundled with SpliceAI; pass a path to score against a custom tab-separated annotation. Changing it restarts the worker. * **`max_distance` (default 50) and `mask` mirror the SpliceAI `-D`/`-M` flags.** Widen `max_distance` to report splice sites farther from the variant; enable `mask` to suppress scores for annotated-gain and unannotated-loss positions.

### SpliceAI Splice-Site Prediction (`spliceai-predict`) Predicts per-position `[neither, acceptor, donor]` probabilities directly from one or more DNA sequences. No reference genome is needed — the model runs on the sequence as given, padding 5,000 bp of context per side internally. #### API Reference

Source DNA sequence(s) to predict on. A single string is auto-wrapped into a list. Sequences may be any length; SpliceAI pads 5000 bp of context on each side internally, so predictions cover every input position.

Source Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run inference on. SpliceAI (TensorFlow) auto-falls-back to CPU when no GPU is visible. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source One entry per input sequence, in input order. Per position, a `[neither, acceptor, donor]` probability triple. Length equals the input sequence's length.

#### Applications Use this to scan an engineered construct, a minigene, or a transcript for latent splice sites, to visualize the acceptor/donor probability landscape across a region of interest, or to compare splice-site usage between designed sequence variants without assembling a genome and annotation. #### Usage Tips * **Output channels are `[neither, acceptor, donor]`.** Index channel 1 for acceptor and channel 2 for donor probabilities; each per-sequence array has the same length as the corresponding input sequence. * **Sequences may differ in length.** They are scored independently (per-item caching applies), so batching ragged sequences is fine; very short sequences still receive the full 10,000 bp `N`-padded context.