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No call samples are displayed as reference homozygous ref(x) / ref (x) #980
Dear JBrowse team,
I think the problem must be around this line (default value is refseq when a splitter is found).
If I use GT = . il my VCF file, the GT column is well formed (i.e. empty) but no-call summary number is now false (because gt is no more an array
Thanks for your help !
I guess the idea is that having a genotype ./. means NO_CALL but jbrowse currently makes it just say reference allele e.g. ref(x)/ref(x) where x is the current letter of the reference genome in the View details popup.
Note that I think ./. was sort of glitchy before this commit db5c5fc but I guess still needs a little work.
Edit: corrected commit