I have a BAM file (hg19) and need to calculate the depth of coverage at each base in the exonic regions. I downloaded the CCDS BED files from the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1109848749_gHXtAmBqKaR1UOA191fS812ba8pn&clade=mammal&org=Human&db=hg19&hgta_group=genes&hgta_track=ccdsGene&hgta_table=0&hgta_regionType=genome&position=chrX%3A15%2C578%2C261-15%2C621%2C068&hgta_outputType=bed&hgta_outFileName=ccds.bed) and used samtools depth
However, I found there are over 900 million bases in the CCDS file, which much exceeds the expected bases in exonic area (roughly 1%). I manually checked the bed file with R and got the similar output of 900 million bases (995030607) for non-overlapping regions
I wonder what the problem might be and I could obtain a BED file obtaining all human exonic regions?
Thank you very much!