June 3, 2024
- show the input variant's VEP consequence in the results table
- the Gencode gene track is now optional in the visualizations
- updated everything to Gencode v46

March 7, 2024
- added warning for insertion variants with delta scores ≥ 0.2 and position = 0bp saying that they may be difficult to interpret due to issue #67. Thanks to @SophieCandille for the issue report and example variant: 2:47790924 C>CAGTTG
- moved server to Google Cloud Run to better support higher usage

November 30, 2023
- changed default search settings to "not masked" due to confusion and issues with how masked scores are computed.
- when looking at hg19 variants, the visualization checkboxes now make it clear which IGV.js tracks are or aren't available on hg19.

October 5, 2023
- fixed Pangolin bug identified by @kazmiekr where variants that overlap more than one gene showed incorrect masked scores
- @pj-sullivan added controls to show/hide transcripts
- added MANE Select transcript labels
- updated to gencode v44 "basic" annotations (instead of comprehensive). These have fewer transcripts per gene.
- added igv.js visualizations

May 22, 2023
- changed defaults to 'masked' and max distance to 500bp
- retired Illumina precomputed scores since they were created using Gencode v24 and max distance = 50bp and so can differ from computed scores which are based on the latest Gencode.

May 12, 2023
- added REF & ALT score columns to show SpliceAI's underlying predictions for each haplotype (using SpliceAI PR by @h-joshi). The Δ  score column is the difference between these two scores.
- added support for MNPs (see issue #1 & SpliceAI PR by @kdahlo)
- updated to Gencode v43 (was previously on v42)

May 10, 2023
- fixed bug where "raw" Pangolin scores were shown regardless of whether the user selected "raw" or "masked".

Feb 5, 2023
- show Pangolin scores in addition to SpliceAI scores.

June 2, 2021
- show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or more matching RefSeq NM ids according to Ensembl. See issue #8 for details.

April 11, 2021
- show gray background for non-coding transcripts
- switch to showing all non-coding transcripts. (Previously, transcripts with Gencode biotypes like lncRNA, processed_pseudogene, processed_transcript, retained_intron, and nonsense_mediated_decay were filtered out if they overlapped protein_coding transcripts). See issue #6 for details.

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Related web tools:
liftover: for variants/positions/intervals (hg19 <=> hg38 <=> T2T)
TGG Viewer: igv.js-based web viewer for public reference tracks and private data in Google Storage buckets. Has custom track types for RNA-seq splice junctions and gCNV variants.