Get aligment quality / identity from CRAM file (for PacBio and ONT data)

Question

[mschmid]

I have PacBio and Oxford Nanopore reads mapped to a reference sequence. Since I have very long reads I had to use CRAM format.

Do you know a nice tool which calculates the aligment quality / mapping identity for every read from the CRAM alignment file?

Idealy it gives me also the the mapping length of the respective mapping.

[h.mon]

How did you align the reads? Most tools able to parse BAM can also parse CRAM, so maybe Picard CollectAlignmentSummaryMetrics may do what you want?

[mschmid]

Partially. But I would like to have it per read. Not an average, to be able to plot a distribution of the alignment quality.