Qualimap does not exclude reads of low mapping quality, while mosdepth does. As a result, coverage computations are currently more optimistic when estimated by qualimap. It would be best to use mosdepth only as this would also improve workflow run-times. It would be best to wait until MultiQC supports mosdepth output, see https://github.com/ewels/MultiQC/issues/924
Qualimap does not exclude reads of low mapping quality, while mosdepth does. As a result, coverage computations are currently more optimistic when estimated by qualimap. It would be best to use mosdepth only as this would also improve workflow run-times. It would be best to wait until MultiQC supports mosdepth output, see https://github.com/ewels/MultiQC/issues/924