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)

Hi,

A blunt approach would be to segregate the alignments first (i.e. before using Gviz) and then display each group separately by creating one AlignmentsTrack object per group. For example separating the soft-clipped alignments from the non-soft-clipped ones could be done by splitting the GAlignments object containing the reads with split(gal, grepl("S", cigar(gal))). The result is a GAlignmentsList object of length 2 with 1 list element per group. To separate the secondary alignments from the primary ones you can either load the 2 groups from the BAM file separately (by calling readGAlignments() twice and passing a ScanBamParam object with the appropriate scanBamFlag() each time) or load all the alignments with the flag field as a metadata column and split the GAlignments object with split(gal, bamFlagAsBitMatrix(mcols(gal)$flag, "isSecondaryAlignment")).

The resulting plot might not be very appealing though so hopefully there is a better way to go...

H.

I guess we could indicate the soft-clipping information for the individual reads in a similar fashion as it is done in IGV. This involves parsing the CIGAR string, and I am not sure how complex that is going to be. Will take a look at this if I find the time, but this is certainly not going to be a quick fix.

Florian