Question marks in Picard output

[Yu-jinKim]

Question

How does MegaQC handle the question marks that you can get in the Picard suite? More specifically how do you store them and how do you handle their plotting?

https://sourceforge.net/p/samtools/mailman/samtools-help/thread/CAEwHMLEAdhWd-C+ELWHZ00NQ5B=UbpK-0DLD21EZjvNL7WOSPQ@mail.gmail.com/

[multimeric]

I haven't tried it myself, but it will ingest whatever MultiQC outputs. The Picard module for MultiQC will have the answers you're after. You can try to run MultiQC on some data with this issue and see what it looks like in the resulting JSON file.

[Yu-jinKim]

They are ingested as I can find the question mark in the multiqc_data.json file. It also looks like they are omitted in the plotting.

Is that the intended behaviour?