Hello, I am running WES samples through gatk based NGS pipeline. I have a BED file limited to exonic intervals. When I use this BED file the variant calling is limited to exonic intervals which saves time but I am concerned that some splicing variants may be excluded. One solution would be to padd the intervals by say 10bp on each side, but I assume this would negatively affect the coverage analysis of the intervals as to my knowledge the coverage is calculated as the average of the provided intervals. Thanks for your feedback.