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investigate-gat-genomic

Investigate GAT (Genomic Association Tester)

Metadata

Statusdone
Assignedagent-72
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-04-01T14:48:56.955826806+00:00
Started2026-04-01T14:50:14.500046901+00:00
Completed2026-04-01T14:55:20.448943332+00:00
Tagseval-scheduled
Eval score0.78
└ blocking impact0.80
└ completeness0.80
└ coordination overhead0.90
└ correctness0.75
└ downstream usability0.75
└ efficiency0.70
└ intent fidelity0.94
└ style adherence0.85

Description

Goal

Investigate GAT (Genomic Association Tester) tool for enrichment analysis in repeat-rich genomic regions.

Specific Questions

  • Is GAT available and installable on the head node?
  • How does it handle repeat-rich regions and multi-copy genes?
  • Input format requirements (intervals, annotations)?
  • Does it work with CHM13 coordinates?
  • Computational requirements and expected runtime?
  • How does its permutation approach compare to custom implementation?

Output

  • GAT availability and installation status
  • Capability assessment for repeat-rich regions
  • Input/output format documentation
  • Runtime and resource requirements
  • Comparison to other permutation-based approaches

Validation

  • GAT installation feasibility confirmed
  • Repeat/multi-copy handling capability documented
  • Input format requirements specified

Depends on

Required by

Log