Someone sent me some BAMs and that is all they sent, so I don't exactly know if they are analysis ready
After some googling I ran Qualimap on all the BAMs. I am wondering what the major QC metrics are to look out for
Mapping rate seemed to be the most obvious to me, looks north of 99% for the most part.
The other main things I seem to read about is duplication rate. It sounds like a high duplication rate could be produced by PCR artifacts. Qulalimap reports
Duplicated reads (flagged) at around 13ish % for many samples.
There are quite a few other metrics, but I am trying to figure out which ones would raise big red flags when looking at BAMs? Is it mostly mapping and duplication rate?