HC Tag

I'm looking at the HC tag that comes out of the --bamOutput option in HaplotypeCaller in the corresponding bam file that is produced. I've noticed that some real reads (i.e. ones not labeled as "ArtificialHaplotype") do not have a HC tag and are NA. What does this mean? That the read was not used and discarded or that no local re-assembly was performed? Many thanks.



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