Large language models for thematic analysis in healthcare research: A blinded mixed-methods comparison with human analysts

Large language models (LLMs) are increasingly used for qualitative thematic analysis, yet evidence on their performance in analysing focus-group data, where polyvocality and context complicate coding, remains limited. Given the increasing role of such models in thematic analysis, there is a need for methodological frameworks that enable systematic, metric-based comparisons between human and model-based analyses. We conducted a blinded mixed-methods comparison of two general-purpose LLMs (ChatGPT-5 and Claude 4 Sonnet), an LLM-based qualitative coding application (QualiGPT), and blinded human analysts on an in-person focus-group transcript informing an AI-enabled digital health proposal. We evaluated deductive coding using a 10-code, 6-theme codebook against an expert consensus adjudication; inductive coding with a structured Likert-scale comparison to a reference-standard set of inductive themes generated by expert consensus; and manual quote verification of LLM segments to define LLM hallucination (evidence absent or non-supportive) and error rate (including partial matches and speaker-coded segments). During deductive coding against an expert consensus adjudication, large language models yielded a mean agreement of 93.5% (95% CI 92.5-94.5) with κ = 0.34 (95% CI 0.26-0.40); blinded human coders achieved 92.7% (95% CI 91.6-93.9) agreement with κ = 0.34 (95% CI 0.26-0.41). Mean Gwet's AC1 was 0.92 (95% CI 0.90-0.93) for the blinded human analysis, and 0.93 (95% CI 0.92-0.94) for the LLM-assisted deductive analysis, reflecting high agreement despite the low overall code prevalence (7.8%, SD = 3.2%). Only one model achieved non-inferiority in inductive analysis of the transcript (p = 0.043). The strict hallucination rate in inductive analysis was 1.2% (SD = 2.1%). LLMs were non-inferior to human analysts for deductive coding of the focus-group data, with variable performance in inductive analysis. Low hallucination but significant comprehensive error rates indicate that LLMs can augment qualitative analysis but require human verification.