I am using Gviz to visualize mappings of PacBio data (bam files) onto contigs. I was wondering if there is any way to display soft-clipped bases at read ends, or at least indicate reads with soft-/hard-clipped ends. That would help a lot in spotting structural variations and potential misassemblies.
Similarly, being able to indicate supplementary alignments of the same query read - e.g. display them in the same way as gapped mappings - would help a lot.
Would be great if anyone had an idea on how this can be done with Gviz. (I am also open to alternative approaches)