Feature suggestions

[delavefm]

It would be a good feature to add the ability to visualize and calculate coverage metrics on regions specified in a BED file. Further, calculation of Fold80base penalty as well.

[fbreitwieser]

Hi @delavefm , I think those are good suggestions. At the moment I excluded BED support since I'd have to take special care of overlapping regions, or rerun the code for each region. Note that you can specify a region on the command line with -r chr:from-to.

Re Fold80base, the definition from Picard: "FOLD_80_BASE_PENALTY: The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.". That's an interesting concept, I can add that.