JBrowse seems to ignore supplementary reads

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JBrowse seems to ignore supplementary reads

Thon deBoer
Hi,

I have a JBrowse implementation (1.11.4, we have not updated to 1.11.5 yet) that has BAM files with a lot of supplementary reads and they do not seem to be counted when you do a SNP Coverage track.
In addition, the mismatches to the reference are NOT showing as the actual mismatch base from the MD tag, but rather are just rendered as grey/gray boxes…

I put in a GitHub entry for this as well but wanted to know if this has been addressed at all in 1.11.5 or if this is a known bug (feature?).

Regards,

Thon

Thon deBoer
Software Product Manager


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