Use GTF/GFF instead of CCDS bed?

[biocyberman]

I have been detached from work that uses chanjo for a while I get outdated when I come back now. It is indeed a good think to see how chanjo quickly develops. I feel the urge of checking coverage for gene/exons/transcripts contained in UCSC's or Ensembl's GTF file. I also know that there are tools (i.e. bedops's gtf2bed) that can covert GTF to BED easily. So the real questions are:

(Q1) How do I use arbitrary BED file from any species or genome build that I use for making my BAM file? What is the workflow? I could not find it in the documentation so I want to make a quick check here. If it is currently not possible, I would like to make it a feature request.

As far as I can see, the benefits of using GTF over CCDS are:

1. GTF is more uptodate than CCDS, so it offer newer annotation information.
2. GTF is free from the constrain of mouse-human relation.
3. it opens up the freedom of using chanjo for all available genomes.

(Q2) Therefore I am curious about the rationale of choosing CCDS over GTF when developing chanjo. I think it has something to do with clinical use in mind.