Standard models for transparency in qualitative research -- providing code and data to produce figures and tables -- map poorly onto qualitative research and writing practices, where evidence is interspersed throughout the text. The Qualitative Data Repository (QDR), in partnership with the software nonprofit Hypothesis, has developed Annotation for Transparent Inquiry to allow authors to create a digital overlay over articles, annotating key passages, and linking them to data sources deposited in a repository. The talk describes some of the ideas behind ATI, takes a closer look at its technical underpinnings, and presents initial results from a study accompanying the generation of recently published pilot projects.