New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

carrere opened this Issue Feb 7, 2018 · 4 comments


None yet
3 participants

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 !



This comment has been minimized.


rbuels commented Feb 7, 2018

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


This comment has been minimized.


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


This comment has been minimized.

carrere commented Feb 8, 2018

@rbuels here is the problem:


This comment has been minimized.

carrere commented Feb 21, 2018

Thanks @rbuels and @cmdcolin ! Works perfectly

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment