diff --git a/index.html b/index.html
index c83f6ac..d657d06 100644
--- a/index.html
+++ b/index.html
@@ -1099,12 +1099,43 @@
"cadd": "CADD",
"revel": "REVEL",
"revel_max": "REVEL",
- "sift_max": "SIFT",
+ "sift_max": "SIFT (max)",
"phylop": "PhyloP",
- "gnomad": "gnomAD",
- "polyphen_max": "PolyPhen",
+ //"gnomad": "gnomAD",
+ "polyphen_max": "PolyPhen (max)",
+ }
+ const gnomADPredictorThresholds = {
+ "revel_max": {
+ "warning": 0.644,
+ "danger": 0.773,
+ },
+ "spliceai_ds_max": {
+ "warning": 0.2,
+ "danger": 0.5,
+ },
+ "pangolin_largest_ds": {
+ "warning": 0.2,
+ "danger": 0.5,
+ },
+ "phylop": {
+ "warning": 7.367,
+ "danger": 9.741,
+ },
+ "sift_max": {
+ "warning": 0.001,
+ "danger": 0,
+ },
+ "polyphen_max": {
+ "warning": 0.978,
+ "danger": 0.999,
+ },
+ "cadd": {
+ "warning": 25.3,
+ "danger": 28.1,
+ },
}
+ //gnomad thresholds: https://github.com/broadinstitute/gnomad-browser/blob/main/browser/src/VariantPage/VariantInSilicoPredictors.tsx#L22-L60
const colorMapForPredictorScores = {
"primateai3d": (record) => {
if (record.percentile >= record.genePercentileThreshold) { // + 0.1) {
@@ -1139,7 +1170,7 @@
return "#ffffff"
}
},
- "revel": (record) => {
+ "revel_max": (record) => {
const score = parseFloat(record.score)
if (score >= 0.773) {
return "#fccfb8"
@@ -1153,11 +1184,11 @@
return "#ffffff"
}
},
- "sift": (record) => {
+ "sift_max": (record) => {
const score = parseFloat(record.score)
if (score < 0) {
return "#fccfb8"
- } else if (score < 0.002) {
+ } else if (score < 0.001) {
return "#fff19d"
} else if (score < 0.081) {
return "#cdffd7"
@@ -1165,7 +1196,7 @@
return "#ffffff"
}
},
- "polyphen": (record) => {
+ "polyphen_max": (record) => {
const score = parseFloat(record.score)
if (score >= 0.999) {
return "#fccfb8"
@@ -1178,8 +1209,14 @@
}
},
"phylop": (record) => {
- //const score = parseFloat(record.score)
- return "#ffffff"
+ const score = parseFloat(record.score)
+ if (score >= 9.741) {
+ return "#fccfb8"
+ } else if (score >= 7.367) {
+ return "#fff19d"
+ } else {
+ return "#ffffff"
+ }
},
"default": (record) => {