I noticed that CallableLoci does not exist in GATK4 anymore, is there a replacement tool for it in GAKT4? Thanks, Luobin
It looks like there are plans to make a new tool for coverage analysis, but it has not happened yet. I am checking with the developer to see if there is an ETA or workaround right now. If you are working with Illumina data, there are quite a few Picard tools you may be interested in. You can find those under Diagnostics and Quality Control in the tool documentation.
I will get back to you soon.
Thank u, @Sheila! Yeah, I basically work on Illumina data.
I'm also looking for an alternative tool of CallableLoci in GATK4. Any suggestion? Thank you.
Have a look at this thread.