Favor Tools

Configuration File: favor_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the favor_tools.json configuration file.

Available Tools

FAVOR_annotate_variant (Type: FAVORVariantAnnotationTool)

Comprehensive functional annotation of a single GRCh38 variant via FAVOR (Functional Annotation o…

FAVOR_annotate_variant tool specification

Tool Information:

  • Name: FAVOR_annotate_variant

  • Type: FAVORVariantAnnotationTool

  • Description: Comprehensive functional annotation of a single GRCh38 variant via FAVOR (Functional Annotation of Variants Online Resource, Harvard). One call returns: allele frequencies (BRAVO/TOPMed, gnomAD by ancestry, 1000 Genomes), gene and consequence (GENCODE category, exonic effect, protein variant, HGVS), deleteriousness scores (CADD, SIFT, PolyPhen-2, AlphaMissense, MetaSVM, MutationTaster/Assessor, FATHMM-XF, Grantham, LINSIGHT, FunSeq), conservation (GERP, phyloP mammalian/primate/vertebrate, phastCons), ClinVar clinical significance/disease, and regulatory/epigenomic context (CAGE promoter/enhancer, GeneHancer, ENCODE DNase, ReMap TF overlap). Use for variant interpretation across both coding and non-coding regions in one step. Input is a GRCh38 (hg38) coordinate string; resolve rsIDs to GRCh38 coordinates first if needed. No API key required.

Parameters:

  • variant (string) (required) GRCh38 SNV/indel as chr-pos-ref-alt. Accepts ‘19-44908822-C-T’, ‘chr19:44908822:C:T’, etc.

Example Usage:

query = {
    "name": "FAVOR_annotate_variant",
    "arguments": {
        "variant": "example_value"
    }
}
result = tu.run(query)