Included in my design files are BED files named target_merged.bed and covered.bed. Which file is relevant for coverage analysis and which for variant calling?

Coverage metrics are analysed using the covered.bed file as this file defines the genomic regions covered by one or more probes, which will extend beyond the target region. Whilst variant calling can be performed with either bed file, the target_merged.bed is considered the better choice. This is because the coverage at the edge of the covered file may be much lower. If you intend to detect splice variants it is advisable to extend your target region at the design stage rather than rely on the extended region of the covered.bed. It is recommended that you visualise your design by loading your bed files as custom tracks in UCSC Genome Browser prior to ordering your panel design.