Hello!
I’m new to these analysis so probably my fault…
These file are not recognized by multiQC, so I added as a first line: ## METRICS CLASS picard.sam.DuplicationMetrics.
At this point I got the following results from MultiQC, which I can see I was checking with Excel, and I only found correspondence with “unmapped” and “duplicate unpaired”. All the other numbers seems to be wrong to me.
Hi,
Would you be able to attach the actual file that you’ve been using with MultiQC?
Could you also share the picard command and picard version that you used to obtain the file? It’s worrying that it doesn’t contain the expected header including the ## METRICS CLASS... line.
Can you also clarify, what numbers do you expect to see?
Note that MultiQC multiplies the “number of pairs” metrics by the factor of 2 to obtain the “number of reads” metrics.
Thanks for clarifying, then it’s all fine!
I saw on your post before you deleted / edited it that you’re using bammarkduplicates. Is that from biobambam2?
In which case feel free to create an issue on the MultiQC GitHub repository about adding official support for this tool, along with some example files. It is likely very little work for us if the files look the same as Picard, then you wouldn’t need to customise anything for them to work with MultiQC, and it’d also benefit other MultiQC users 
Thanks!