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Question: Color / mark specific sequence bases differently in IGV
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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!

ADD COMMENTlink 5.2 years ago Matt Shirley 9.0k • updated 5.1 years ago Biostar 20
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Quick question: Can you point me to documentation about the YC tag?

A follow-up: We could probably add a simple plug-in to IGB (bioviz.org) that would enable color-coding bases using a YY:B: attribute. Already there is a mechanism to color-code bases by score, so adding this would not be too hard. IGB also supports SAM. (No need to make an index.)

ADD REPLYlink 5.2 years ago
Ann
♦ 2.2k
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Certainly. The UCSC documentation for that tag is here: http://genome.ucsc.edu/goldenpath/help/hgBamTrackHelp.html. Don't take me literally about designating a "YY" tag with a byte array type code, as this is just a hypothetical example.

ADD REPLYlink 5.2 years ago
Matt Shirley
9.0k
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Keep in mind that since tags beginning with Y are custom, it's likely that some aligner already uses that (though probably not with a byte array). This might be a good excuse to add a new auxiliary tag to the specification.

ADD REPLYlink 5.2 years ago
Devon Ryan
90k
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:) Yes, I already struggle with other people using X/Y/Z prefix tags. In fact, it seems like some of the X-prefix tags have become standardized enough that they should have been included elsewhere in the tag namespace of the specification.

ADD REPLYlink 5.2 years ago
Matt Shirley
9.0k
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Yeah, the XS tag is a good example of that.

ADD REPLYlink 5.2 years ago
Devon Ryan
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