We have decided to continue providing and supporting DepthOfCoverage and DiagnoseTargets for the foreseeable future. Going forward, we'll try to integrate them and develop their features to address the main needs of the community. To this end we welcome your continuing feedback, so please feel free to contribute comments and ideas in this thread.
To all who took the time to tell us what you find useful about DoC and DT (and what you wish it could do), a big thank you! This is always very useful to us because it helps us identify which features are most valuable to our users.
Now that DepthOfCoverage is being retired in GATK 2.4, I decided to investigate DiagnoseTargets. I have some questions.
1) Are there plans to support output formats other than VCF? What was great about DOC is I could easily send the output to anyone and it could be easily read. With DT, that requires additional processing.
2) DOC provided summary for intervals as well as samples. DT only does intervals. Is there a way to get per-sample info?
3) DOC output full intervals. DT only outputs the start positions. To get the end positions, an additional step is required. Can that be adjusted?
4) DOC provided coverage info for all intervals. DT only shows covered intervals, so if an interval is not covered, it will not be listed in the output. Is there a way to output all intervals?
Sorry if I sound too critical. I am a big fan of DepthOfCoverage and am disappointed to see it go.