AutoPVS1 through GeneFoundry

Router invocation: autopvs1_get_server_capabilities()

Use this to discover AutoPVS1-Link MCP tools, inputs, limitations, and workflow.

Router invocation: autopvs1_get_server_health()

Return local MCP server health. Default behaviour: no upstream call, sub-millisecond. Pass ``check_upstream=true`` for an opt-in HEAD probe — useful when an agent wants to confirm AutoPVS1 is reachable before scheduling a cold scoring call.

Router invocation: autopvs1_get_variant_pvs1_data()

Score one SNV/indel variant with the AutoPVS1 PVS1 rules. Auto-resolves non-canonical inputs (rsID, HGVS c./p./g.) into canonical SPDI via one Ensembl Variant Recoder REST call before scoring (build-scoped — GRCh37 host for hg19, GRCh38 host for hg38). Emits an ``auto_resolved`` warning carrying the input, the resolved id, and the resolver source. Ambiguous resolutions return ``error_code='ambiguous_query'`` (subcode ``requires_disambiguation``) with allele-keyed candidates instead of silently picking one (mitigates multi-allelic mis-scoring). First-turn LLM callers get the verdict under ~1.5KB by default (``response_mode='summary'``). Widen to ``response_mode='standard'`` for the full decision tree, or ``'full'`` for the audit-trail ``*_raw`` upstream fields. AutoPVS1 outputs are research-use only, not clinical decision support.

Router invocation: autopvs1_get_cnv_pvs1_data()

Score one copy-number variant with the AutoPVS1 PVS1 rules. First-turn LLM callers get the verdict under ~1.5KB by default (``response_mode='summary'``). Widen to ``response_mode='standard'`` for the full decision tree. AutoPVS1 outputs are research-use only, not clinical decision support.

Router invocation: autopvs1_get_variants_pvs1_data_bulk()

Score 1-10 SNV/indel variants in one call. Prefer this over ``get_variant_pvs1_data`` when you have 2+ variant IDs of the same kind. For LLM batch screens, default to ``response_mode='summary'`` so 10 verdicts share one turn budget; widen per-item only when reasoning needs the full decision tree. Items run sequentially server-side and respect the upstream rate limit (default ~1 req/s) plus the existing cache, so a fully uncached 10-item batch can take ~10s wall time and a fully cached one returns in milliseconds. Auto-resolution applies per item: non-canonical inputs (rsID, HGVS c./p./g.) round-trip through Ensembl Variant Recoder before scoring, mirroring ``get_variant_pvs1_data``. Multi-candidate resolutions return per-item ``requires_disambiguation`` with allele-keyed candidates so the caller picks one and re-calls that single item; a resolver outage returns the retryable ``external_resolver_unavailable`` code. Per-item envelope: each row in the top-level ``results`` array has ``{ok, input, data, error, meta}`` where ``meta.cache_status`` and ``meta.elapsed_ms`` echo that one upstream call's outcome (absent when the item short-circuited before upstream). This per-item shape predates and is scoped separately from the Response-Envelope Standard v1 outer frame. Output items preserve input order. ``response_mode`` and ``include_unmet`` apply per item; the outer ``meta_mode`` controls the envelope. Per-item failures do not stop the batch unless ``continue_on_error=false``. Bulk dispatch errors (malformed ``items``) use ``error_code='invalid_input'`` (subcode ``invalid_bulk_input``). Aggregate cache observability: top-level ``_meta.cache_status`` echoes the unanimous status when every item agrees; on a mixed batch it is ``"mixed"`` and ``_meta.cached_count`` / ``_meta.uncached_count`` split items by warm (``hit``+``coalesced``) vs cold (``miss``+``bypass``). ``_meta.elapsed_ms`` is the SUM of per-item upstream wall-clocks (the honest total for a sequential bulk). Warning aggregation: per-item warnings are NOT echoed; they are collapsed into ``_meta.warnings`` at the top level. A warning code is aggregated only when more than one distinct item emitted it; single-item codes appear without ``count`` or ``affected_indices``. Aggregated codes carry ``count`` (distinct items) and the sorted ``affected_indices`` list. Order is first-seen-code-first.

Router invocation: autopvs1_get_cnvs_pvs1_data_bulk()

Score 1-10 CNVs in one call. Prefer this over ``get_cnv_pvs1_data`` when you have 2+ CNV IDs. For LLM batch screens, default to ``response_mode='summary'`` so 10 verdicts share one turn budget. Same semantics as ``get_variants_pvs1_data_bulk``: sequential server-side, respects upstream rate limit + cache; per-item ``{ok, input, data, error, meta}`` with ``meta.cache_status`` + ``meta.elapsed_ms`` echoing each item's upstream outcome; output items preserve input order; ``response_mode`` and ``include_unmet`` apply per item; the outer ``meta_mode`` controls the envelope. Per-item failures do not stop the batch unless ``continue_on_error=false``. Aggregate cache observability: top-level ``_meta.cache_status`` is ``"mixed"`` when items had varied outcomes (with ``cached_count`` / ``uncached_count``) or echoes the unanimous status. ``_meta.elapsed_ms`` is the SUM of per-item upstream wall-clocks. Warning aggregation: per-item warnings collapse into ``_meta.warnings``; codes emitted by more than one distinct item carry ``count`` and ``affected_indices``; single-item codes do not. Order is first-seen-code-first.

Router invocation: autopvs1_search_variants()

Search AutoPVS1 by gene symbol or variant text. Use ``response_mode='ids_only'`` (lowest-bandwidth lookup) to resolve a query to an AutoPVS1 ``variant_id`` you can hand to ``get_variant_pvs1_data``. ``next_cursor`` is base64url JSON today (decodable) but treat it as an echo-back token; it MAY become opaque later. AutoPVS1 outputs are research-use only, not clinical decision support.