Get aligment quality / identity from CRAM file (for PacBio and ONT data)
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.
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How did you align the reads? Most tools able to parse BAM can also parse CRAM, so maybe
Picard CollectAlignmentSummaryMetricsmay do what you want?Partially. But I would like to have it per read. Not an average, to be able to plot a distribution of the alignment quality.