pb-CpG-tools doesn't emit a methylaton score despite evidence of modified 5mC bases

[indapa]

Hi PacBio team

I have an example where I don;t have a CpG score on a site, despite having evidence of modified 5mC base (colored in red) There is only 8 reads covering the position. Can you help me understand why a score isn't emitted?

[indapa]

Another question - but this may be an IGV one. Does the blue represent base modification probability less than a certain threshold? Similar to my previous question, cpG tools doesn't emit a score though there is some evidence of a modified base in red.

[ctsa]

@indapa - Expectations for seeing a site score from this example depends on the min-coverage level used for pb-CpG-tools. If you run directly form the default values the min-coverage is 4. If your sites track is obtained from the WGS wdl pipeline I believe the default min-coverage set there has been 10, this could be one possible explanation for your case.

[ctsa]

Re IGV, blue is the default color for unmodified bases -- there's been a lot of recent feature improvement in this area for IGV so I'd check with the latest docs, the current wiki clarifies that it starts the blue gradient at 50%:

https://github.com/igvteam/igv/wiki/5mC-coloring-mode