281685b26873cd6651852667145c7050e7f5c907 gperez2 Mon Oct 13 16:58:17 2025 -0700 Code review edits, refs #36502 diff --git src/hg/makeDb/trackDb/human/spliceImpactSuper.html src/hg/makeDb/trackDb/human/spliceImpactSuper.html index d7caf04cbfc..ea2669ce8bd 100644 --- src/hg/makeDb/trackDb/human/spliceImpactSuper.html +++ src/hg/makeDb/trackDb/human/spliceImpactSuper.html @@ -24,33 +24,33 @@ learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. To score variants, the spliceAI algorithm is run on the genome sequence itself and scores each nucleotide for the probability that it is a donor or acceptor site, on both the forward and the reverse strand. Then variants are added to the sequence and the new sequence is scored. Variants may activate nearby cryptic splice sites, leading to abnormal transcript isoforms. SpliceAI was developed at Illumina; a <a href="https://spliceailookup.broadinstitute.org" target="_blank">lookup tool</a> is provided by the Broad institute. </p> <h3>SpliceAI Wildtype</h3> <p> This SpliceAI "Wildtype" container track shows the scores for the genome sequence itself, without variants, from predicted splice donor (5' intron boundaries) and splice acceptor (3' intron boundaries) sites. Predictions are strand-specific, with separate subtracks for the -plus and minus strands. These tracks are useful when looking at new transcript models to evaluate -how likely exon boundaries are and where possible splice acceptor sites are, in combination with -the variants track.</p> +plus and minus strands. These tracks are useful in combination with the variants track for +evaluating new transcript models. They can be used to assess potential exon boundaries or +possible splice acceptor sites.</p> <b>Why are some variants not scored by SpliceAI?</b> <p> SpliceAI only annotates variants within genes defined by the gene annotation file. Additionally, SpliceAI does not annotate variants if they are close to chromosome ends (5kb on either side), deletions of length greater than twice the input parameter -D, or inconsistent with the reference fasta file. </p> <b>What are the differences between masked and unmasked tracks?</b> <p> The unmasked tracks include splicing changes corresponding to strengthening annotated splice sites and weakening unannotated splice sites, which are typically much less pathogenic than weakening annotated splice sites and strengthening unannotated splice sites. The delta scores of such splicing changes are set to 0 in the masked files. We recommend using the unmasked tracks for alternative