e0d0dd65f53bb547c201ae1aa2bf0fa6dbbafe09 max Thu Jun 3 08:25:17 2021 -0700 changes after code review, refs #27648 diff --git src/hg/makeDb/trackDb/human/revel.html src/hg/makeDb/trackDb/human/revel.html index df7d611..688b467 100644 --- src/hg/makeDb/trackDb/human/revel.html +++ src/hg/makeDb/trackDb/human/revel.html @@ -28,32 +28,32 @@ <p> For single nucleotide variants (SNV), at every genome position, there are three values per position, one for every possible nucleotide mutation. The fourth value, "no mutation", representing the reference allele, e.g. A to A, is always set to zero. <br> When using this track, zoom in until you can see every basepair at the top of the display. Otherwise, there are several nucleotides per pixel under your mouse cursor and no score will be shown on the mouseover tooltip. </p> <p>For hg38, note that the data was converted from the hg19 data using the UCSC liftOver program, by the REVEL authors. This can lead to missing values or duplicated values. When a hg38 position is annotated with two scores due to the lifting, the authors removed all the scores for this position. They did the same when -due to a reference change a mutation in hg19 is not a mutation in hg38 anymore, but the -reference nucleotide. Also, on hg38, the track has the "lifted" icon to indicate +the reference allele has changed from hg19 to hg38. Also, on hg38, the track has +the "lifted" icon to indicate this. You can double-check if a nucleotide position is possibly affected by the lifting procedure by activating the track "Hg19 Mapping" under "Mapping and Sequencing". </p> <h2>Data access</h2> <p> REVEL scores are available at the <a href="https://sites.google.com/site/revelgenomics/" target="_blank"> REVEL website</a>. The site provides precomputed REVEL scores for all possible human missense variants to facilitate the identification of pathogenic variants among the large number of rare variants discovered in sequencing studies. </p>