We propose to use the unique event topology and reconstruction capabilities of liquid argon time projection chambers to study sub-GeV atmospheric neutrinos. The detection of low energy recoiled protons in DUNE allows for a determination of the leptonic $CP$-violating phase independent from the accelerator neutrino measurement. Our findings indicate that this analysis can exclude several values of $delta_{CP}$ beyond the $3sigma$ level. Moreover, the determination of the sub-GeV atmospheric neutrino flux will have important consequences in the detection of diffuse supernova neutrinos and in dark matter experiments.
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