We have performed a targeted sequencing of a few megabases of human DNA on ~20 samples using Illumina GA2. I've done alignment and genotyping, but I know our targeting method (SureSelect) has coverage gaps where no reads will align. I would like to identify these gaps from the aligned reads. My end goals are:
1) Summary statistics of coverage depth for each sample
2) Identify regions where I have no coverage in any sample
3) Able to generate ad hoc plots of coverage depth using tools of my own choice
Before I put my nose down and start coding off of the SAM pileup format, has someone written a package (or function in a package) that solves this problem for me? I'd rather use someone else's debugged code than write my own. I'm not looking to install a web server and click around; my ideal output would be a matrix where each row is a locus and each column is a sample, with number of mapped reads as the matrix value.