gene.iobio

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Show warning when vcf URL missing for mother/father in trio

1

Load demo data. Now go to 'Files' dialog and select a file for mother. Now reload the browser window. Instead of warning user and bringing up 'Files' dialog, the first...

tonydisera

Joint calling on gene returns variant outside of specified region

1

Joint call variants returns a variant that is outside of MTHFR gene range (platinum whole genome) SNP 11844737 (see screen print)

tonydisera

After user has performed 'Analyze All' on a set of genes and then adds new genes, warn user that not all genes have been analyzed.

1

tonydisera

Allele count scaling

4

It would be better to set the scale for the allele counts to fill the tooltip.

AlistairNWard

gene.iobio picked ENST00000274990.4 as the canonical. But Ensembl shows ENST00000372569.7 as the first transcript. Also, refseq chose the same equivalent for the canonical NM_206922.2. I suspect that gene.iobio is using...

tonydisera

Zooming into high density variant region (e.g. Clinvar) shows overlapped symbols in variant card

2

Zoom into a region of Clinvar Variants. Now the variant symbols overlap. http://gene.iobio.io/?rel0=proband&rel1=mother&rel2=father&gene=TP53&name0=proband&name1=mother&name2=father&sample1=10718X3&sample2=10718X2&genes=TP53&affectedSibs=&unaffectedSibs=&vcf0=https://s3.amazonaws.com/vcf.files/clinvar_20161003.vcf.gz

tonydisera

You should not be able to "x" out the gene badge for the gene you are currently viewing.

2

Allowing this can lead to some weird states when x'ing out and adding new genes.

nielsonphu

Data entry modal problems

3

1. Open gene and select platinum data for a trio. Click load and all panels are displayed as expected. 2. Go back to the Data modal. 3. Click 'Single'. The...

AlistairNWard

The tooltip shows 'multi-allelic' counts in the allele count bar, but it isn't prominent. Need a way to draw attention to multi-allelics.

tonydisera

When looking in some genes, there are no ClinVar variants, but with no counts it isn't always obvious if there are none, or that they failed to load. For example,...

AlistairNWard