I have some questions here. I want to do some quality control analysis on my exome data that are mapped on the reference genome. I am having the input bam file for a sample which contains reads that got mapped to reference genome(hg19.fa). So it is like my mapped reads are 80 million for this sample. Now I want to calculate out of this 80 million mapped reads how many got mapped into the exome region. For this I need to supply the exome baits bed file (probe/covered.bed) provided by the company. We used the Agilent SureSelectV4 here. So is there any one line command with which using these three informations (input.bam, hg19.fa and exome_baits.bed) I can calculate the total number of mapped reads on the exonic regions? Any one line command. In different posts I see a lot of tools being mentioned. I tried to used CalculateHSmetrics of Picard but it needs the bed file with header so of now use now. Then I used the walker of GATK which is the DepthofCoverage but there we usually get the mean of number of time a bases is read(for me its 73.9) and the %_of_bases_reads above 15 times is about 70% which is also a good qaulity, we also get how many loci has been read more than once which gives a histogram of cumulative reads coverage at each loci but if I want to just calculate the number of mapped reads that got mapped in the exome region using the input bam file, reference genome and exome_baits.bed file how shall I do it? Any single line command for that? This might be recurrent but am not getting any specific answer in the forums so I had to post. Any suggestions?