I have a mapped BAM file that contains 32 samples and 20 genes from a targeted re-sequencing experiment ran on a 316 ion torrent chip. Is there a way I can calculate the individual sample sequencing depth at each gene instead of all of the samples together? I used IGV to generate coverage data, but the result is all samples combined. I'm not sure if graphically is best since even exon to exon the same sample seems to have variation in depth. Or maybe a min, max, mean depth for each sample at each gene is the right way to look at it?
Also, I've been searching Biostar to get a feel for the standard depth required for SNV calling on a targeted re-sequencing project; while I couldn't find a definitive standard, I get the feeling ~30x depth is a good place to start... any thoughts?
Update: After doing some more searching, maybe the approach needed is a by-amplicon depth analysis. Meaning, at each amplicon generate the mean, std dev, min & max depth across all samples.
Update2 I used coveragebed in BEDtools to figure out how many reads in my BAM map to a BED of each amplicon and also a base by base depth report using the '-d' option. But this still would leave me doing manual mean, min, max, stddev calcs on ~720 amplicons. There must be some tool to look at the data this way right? That or perhaps I should be looking at depth data another way for a project of this type.