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BixBench item

bix-20-q3

Question

Among samples with a 'Carrier' BLM mutation status, what proportion of somatic CHIP variants (VAF < 0.3) with ClinVar classifications are classified as Benign or Likely Benign? The proportion of somatic CHIP variants should be calculated after filtering out intronic, intergenic, UTR regions, and reference (non-variant) calls.

Ideal answer
(0.80, 1.00)
Category
Genomics,Genomic Variant Analysis

Galaxy-API code with skills

3/3 pass

Galaxy-API code without skills

3/3 pass

Open-ended code with skills

3/3 pass

replicate 1

pass
Answer1
Workflow
local codecompute_answer.py
No Galaxy historyHugging Face trace

replicate 2

pass
Answer1
Workflow
local codeverification note
No Galaxy historyHugging Face trace

replicate 3

pass
Answer1.0
Workflow
local codeverification note
No Galaxy historyHugging Face trace

Open-ended code without skills

3/3 pass

replicate 1

pass
Answer1.0
Workflow
local codecompute_answer.py
No Galaxy historyHugging Face trace

replicate 2

pass
Answer1.0
Workflow
local codeverification note
No Galaxy historyHugging Face trace

replicate 3

pass
Answer1.0
Workflow
local codecompute_answer.py
No Galaxy historyHugging Face trace