Sometimes I've interested in highlighting specific positions within the sequence fields of a BAM file using something like IGV. Is there any standardized way to accomplish this with e.g. a SAM tag such as:
YY:B:(array of integers specifying positions to highlight)
In general there seems to be a lack of display and styling metadata for SAM, and given that formats like BED have numerous (sometimes loosely defined) styling options (see UCSC color format). FWIW I'm aware of the UCSC-sanctioned "YC" tag, which sets the color for the entire alignment and is recognized in IGV, but I'm thinking of something that would affect only certain positions in the alignment. Thanks!