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No call samples are displayed as reference homozygous ref(x) / ref (x) #980

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carrere opened this Issue Feb 7, 2018 · 4 comments

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@carrere

carrere commented Feb 7, 2018

Dear JBrowse team,
I noticed that sample without variant calling (GT = ./.) are not well displayed in the detail table . Column GT is set to ref(x) /ref(x) where x is the reference nucleotide.

I think the problem must be around this line (default value is refseq when a splitter is found).

return gtIndex ? ( alt ? alt[gtIndex-1] : gtIndex ) : refseq;

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

if( lang.isArray( gt ) ) {
)

Thanks for your help !

Sebastien

@rbuels

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rbuels commented Feb 7, 2018

@carrere could you also attach a screen shot of what the problem looks like in the detail box?

@cmdcolin

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cmdcolin commented Feb 7, 2018

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

@carrere

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carrere commented Feb 8, 2018

@rbuels here is the problem:
nocall

@carrere

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carrere commented Feb 21, 2018

Thanks @rbuels and @cmdcolin ! Works perfectly

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