: issues or feature requests for this website
- provide a table with detailed SpliceAI scores for insertion variants whenever donor or acceptor gain is predicted to occurs within the inserted sequence itself. This addresses
MAJOR BUG FIX: Between April and November of 2024,
Pangolin scores were incorrectly computed for ~28% of hg38 variants and ~5% of hg19 variants due to a bug related to multiple requests being processed in parallel. This issue has now been fixed.
SpliceAI scores were fine and were not affected by this bug.
November 3, 2024
- added choice of Gencode
basic or comprehensive transcripts
- updated to Gencode v47
June 20, 2024
- fixed SpliceAI visualizations to clarify positions of predicted splicing changes. See
issue #70 for details.
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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