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Unknown BAM tag type 'B', tags may be incomplete #568
I think JBrowse doesn't dig the extra information padded in Ion Torrent BAM files. Is there anything that can be done to make it ignore the offending tags and display the base changes correctly? It seems to read the CIGAR a-OK as I can see locations of indels.
I can't fix this but I can diagnose for someone who has the JS skills. There is nothing wrong with your BAM records (according to the spec):
It looks like this has been in the spec since 2011, but I don't know when the core BAM parsing code was written:
P.S. Although there's nothing wrong with the format of the SAM record I'd be a little concerned about it being mapped (even with MAPQ=0) with only 4/26 bases matching and 5 soft clipped.