I have read somewhat contradictory things across the documentation as to what DP actually measures, and I can't quite tell if I'm missing some distinction between the "different" DPs. I have read that DP is the filtered read depth to only what HaplotypeCaller finds informative (as stated in the DepthPerSampleHC DP annotation documentation and therefore will likely exclude things like PCR duplicates) but I have also read that it does not filter out to only reads found informative by HaplotypeCaller (as stated in the Coverage DP annotation documentation and in this forum discussion https://gatkforums.broadinstitute.org/gatk/discussion/comment/11861#Comment_11861 which states “Keep in mind that the depth reported in the DP field of the VCF is the unfiltered depth”).
I continue to be confused by this and I’d really like a more clear answer as to what the DP annotation for the sample-level actually includes. Is DP at the sample-level unfiltered, partially filtered, or filtered all the way down to reads only found informative by HaplotypeCaller?
I continue to be confused by this and I’d really like a more clear answer as to what the DP annotation for the sample-level actually includes. Is DP at the sample-level unfiltered, partially filtered, or filtered all the way down to reads only found informative by HaplotypeCaller?