Please let me know what happened to Callable Loci; I do not see it in GATK 4's list of tools.
Thank you for your assistance.
Have a look at this thread. It seems there is not much demand to port the other coverage tools, so you may try using the ones in GATK3.
Thank you for your reply. GATK 3.8's CallableLoci program has been very helpful when, for instance, I want to see where no coverage occurs - as well as frequency of no calls - when I analyze a BAM file's Y chromosome coverage.
We have made porting the coverage tools a higher priority. I think the plan is to have a tool that outputs what you want plus some other coverage functionalities that others may want. You can keep track of the issue here.
Thank you for your reply.
Until the coverage tools are ported, I was thinking of using CallableLoci from GATK3.8 as part of an analysis in which everything else is done with GATK4. CallableLoci seemed to me like a standalone tool that ought to work (assuming read filters etc are checked) regardless of the version of GATK used to call the SNPs, but I was worried that I might be missing something. Is your answer saying it should probably be ok to use this GATK3 tool along with a GATK4 analysis, or were you suggesting that if we want to use it we should stick with GATK3 for everything? Thanks!
It is fine to use GATK3 tools for coverage analysis even if you use GATK4 tools for everything else. I realize this is a phase where things are still being ported over, but most tools in GATK4 still output very similar results to GATK3, so you will be fine
Thanks for your reply, that's just what I wanted to hear!