Pragmatic clinical trials (PCTs) evaluate interventions in real-world settings, often using electronic health records (EHRs) for efficient data collection. We report on the challenges in performing EHR analysis of healthcare provider orders in a PCT within the eMERGE consortium, which investigates the impact of reporting genome-informed risk assessments (GIRA) to over 25,000 patients across 10 academic medical centers. Clinical informaticians conducted a landscape analysis to identify approaches for evaluating the outcomes of GIRA reporting through the EHR. Of 98 identified outcomes, 54 (55.1%) were determined to be difficult to extract because they involved provider orders, which are typically documented in free text or proprietary formats within the EHR and only mapped to standardized codes after the service is completed. These findings highlight a critical barrier in using EHRs to support PCTs. The authors recommend closer collaboration between clinicians and informaticians, improved EHR systems that support standardized order entry, and future use of machine learning to automate analysis of provider behavior in clinical trials.