UCSC genome track displays the wrong transcript variant

[Peter-J-Freeman]

Describe the bug

Variant: 1:40091393:T:A Hello, I noticed a problem concerning UCSC genome browser VariantValidator tracks for all variants. 1) when searching for a variant with genomic coordinates 2) which leads to requirement to choose a transcript or transcripts (for this variant 1:40091393:T:A either NM_000310.4, NM_001142604.2 or NM_001363695.2) 3) and then when trying to follow "View variant in external resources - UCSC Genome Browser" link, for every variant only the track for the first one in the list, here NM_000310.4, is shown. So when I am on a tab to show the variant as NM_001142604.2:c.125-1881A>T, the UCSC Genome Browser link still shows me "VariantValidator track for NM_000310.4:c.369A>T" I have tested this with other variants; for example 1:75761161:A:G, where all transcript options provide UCSC Genome Browser link only for the first one in the list, "VariantValidator track for NM_000016.6:c.985A>G" When providing the search term as NM_001142604.2:c.125-1881A>T, the correct UCSC Genome Browser "VariantValidator track for NM_001142604.2:c.125-1881A>T" is shown.

[Peter-J-Freeman]

This is indeed a bug. Thanks

[Peter-J-Freeman]

Mostly resolved. Some variants fail. See https://github.com/openvar/variantValidator/issues/518

[Peter-J-Freeman]

OK, all fixed except that if the orientation for the transcript cannot be calculated, probably because its not actually mapped to a specific build but we lift over, then no transcript track is displayed.