Borzoi Calico Tools#

Configuration File: remote_tools/borzoi_calico_tools.json Tool Type: Remote Tools Count: 1

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

Available Tools#

run_borzoi_calico_sad (Type: RemoteTool)#

Score regulatory variants with CALICO’S OWN Borzoi release (borzoi_sad.py at commit 5c93582, fold…

run_borzoi_calico_sad tool specification

Tool Information:

  • Name: run_borzoi_calico_sad

  • Type: RemoteTool

  • Description: Score regulatory variants with CALICO’S OWN Borzoi release (borzoi_sad.py at commit 5c93582, fold 0, reverse-complement ensemble) against pinned GRCh38. Returns upstream’s four published statistics – SAD, logSAD, D2, logD2 – over 6,385 strand-summed human RNA tracks, with the strongest tracks per variant named. This is the paper’s method rather than an approximation of it; use run_borzoi_variant_effect (the borzoi-pytorch port, GPU) for a fast central-bin delta from two sequences. CPU-only here: about four minutes per variant, four variants maximum.

Parameters:

  • variants (array) (required) Single-nucleotide variants to score, at most 4. Each costs about four minutes.

  • top_tracks (integer) (optional) How many tracks to name per variant, ranked by |SAD|. The full 6,385-track vectors stay in the provider’s sad.h5, whose path the reply carries.

Example Usage:

query = {
    "name": "run_borzoi_calico_sad",
    "arguments": {
        "variants": ["item1", "item2"]
    }
}
result = tu.run(query)