Forge Tools gtex_splice_qtl

gtex_splice_qtl read

scidex.forge.gtex_splice_qtl

Query GTEx v8 cis-sQTL associations — genetic variants that regulate alternative splicing events in specific human tissues. Accepts a gene symbol (e.g. TP53, MAPT) and optional tissue filter (e.g. Whole_Blood, Brain_Cortex). Returns significant sQTL records with variant ID, intron cluster (phenotype), p-value, and normalized effect size (NES). Distinct from gtex_eqtl (expression QTL) — sQTLs map variants to splicing changes, not expression levels, with different disease mechanism implications. GTEx v8 has ~24K significant sQTL pairs per gene on average. REST API: https://gtexportal.org/api/v2/ — free, no auth.

HTTP: POST /api/scidex/forge/gtex_splice_qtl

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.gtex_splice_qtl``.",
  "properties": {
    "gene": {
      "description": "HGNC gene symbol to look up sQTLs for (e.g. ``TP53``, ``MAPT``).",
      "maxLength": 50,
      "title": "Gene",
      "type": "string"
    },
    "tissue": {
      "default": "Whole_Blood",
      "description": "GTEx tissue site detail ID (e.g. ``Whole_Blood``, ``Brain_Cortex``). Defaults to ``Whole_Blood``.",
      "maxLength": 100,
      "title": "Tissue",
      "type": "string"
    },
    "dataset_id": {
      "default": "gtex_v8",
      "description": "GTEx dataset version (default ``gtex_v8``).",
      "maxLength": 30,
      "title": "Dataset Id",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of sQTL records to return (default 20, max 250).",
      "maximum": 250,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgeGtexSpliceQtlIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "SpliceQtlHit": {
      "description": "One GTEx cis-sQTL association record.",
      "properties": {
        "variant_id": {
          "description": "GTEx variant identifier (e.g. ``chr17_7661779_A_G_b38``).",
          "title": "Variant Id",
          "type": "string"
        },
        "phenotype_id": {
          "description": "GTEx phenotype identifier — encodes the intron cluster (e.g. ``ENSG00000141510.11_17_7661779_7661981_clu_27580_-``).",
          "title": "Phenotype Id",
          "type": "string"
        },
        "intron_cluster": {
          "description": "Intron cluster identifier extracted from phenotype_id (e.g. ``clu_27580_-``).",
          "title": "Intron Cluster",
          "type": "string"
        },
        "p_value": {
          "description": "Nominal p-value for the sQTL association.",
          "title": "P Value",
          "type": "number"
        },
        "nes": {
          "description": "Normalized effect size: allelic fold change in intron excision ratio per copy of the alternative allele.",
          "title": "Nes",
          "type": "number"
        },
        "tissue": {
          "description": "GTEx tissue site detail ID (e.g. ``Whole_Blood``).",
          "title": "Tissue",
          "type": "string"
        },
        "chromosome": {
          "description": "Chromosome extracted from variant_id (e.g. ``chr17``).",
          "title": "Chromosome",
          "type": "string"
        },
        "position": {
          "description": "Genomic position (bp) extracted from variant_id.",
          "title": "Position",
          "type": "integer"
        }
      },
      "required": [
        "variant_id",
        "phenotype_id",
        "intron_cluster",
        "p_value",
        "nes",
        "tissue",
        "chromosome",
        "position"
      ],
      "title": "SpliceQtlHit",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.gtex_splice_qtl``.",
  "properties": {
    "gene": {
      "description": "The gene symbol queried.",
      "title": "Gene",
      "type": "string"
    },
    "tissue": {
      "description": "The tissue filter applied.",
      "title": "Tissue",
      "type": "string"
    },
    "dataset_id": {
      "description": "The GTEx dataset version used.",
      "title": "Dataset Id",
      "type": "string"
    },
    "sqtl_hits": {
      "description": "Matching cis-sQTL association records, sorted by p-value ascending.",
      "items": {
        "$ref": "#/$defs/SpliceQtlHit"
      },
      "title": "Sqtl Hits",
      "type": "array"
    },
    "top_variant": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "variant_id of the most significant sQTL hit (lowest p-value), or None.",
      "title": "Top Variant"
    },
    "not_found": {
      "default": false,
      "description": "True when the gene symbol could not be resolved or returned no sQTL data.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "gene",
    "tissue",
    "dataset_id"
  ],
  "title": "ForgeGtexSpliceQtlOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/gtex_splice_qtl' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene": ""
}'

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