Add API support for exome FAFMax

broadinstitute · May 10, 2024 · 4503a94 · 4503a94
1 parent 61ea796
commit 4503a94
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Showing 2 changed files with 11 additions and 8 deletions.
diff --git a/graphql-api/src/graphql/types/variant.graphql b/graphql-api/src/graphql/types/variant.graphql
@@ -99,6 +99,13 @@ type LoFCuration {
   project: String!
 }
 
+type Fafmax {
+  faf95_max: Float
+  faf95_max_gen_anc: String
+  faf99_max: Float
+  faf99_max_gen_anc: String
+}
+
 type VariantSequencingTypeData {
   ac: Int
   an: Int
@@ -107,6 +114,7 @@ type VariantSequencingTypeData {
   filters: [String!]
   populations: [VariantPopulation]
   faf95: VariantFilteringAlleleFrequency
+  fafmax: Fafmax
 
   # Deprecated - calculate from AC and AN
   # Preserved for compatibility with existing browser queries
@@ -117,21 +125,14 @@ type VariantSequencingTypeData {
   ac_hemi: Int
 }
 
-type JointFafmax {
-  faf95_max: Float
-  faf95_max_gen_anc: String
-  faf99_max: Float
-  faf99_max_gen_anc: String
-}
-
 type VariantJointSequencingTypeData {
   ac: Int
   an: Int
   homozygote_count: Int
   hemizygote_count: Int
   filters: [String!]
   populations: [VariantPopulation]
-  fafmax: JointFafmax
+  fafmax: Fafmax
 }
 
 type NonCodingConstraintRegion {

diff --git a/graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts b/graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts
@@ -309,6 +309,7 @@ const shapeVariantSummary = (subset: Subset, context: any) => {
               (pop: any) => !(pop.id.includes('_') || pop.id === 'XX' || pop.id === 'XY')
             ),
             filters: exomeFilters,
+            fafmax: variant.exome.fafmax[subset],
           }
         : null,
       genome: hasGenomeVariant
@@ -349,6 +350,7 @@ const getMultiVariantSourceFields = (
     `value.genome.freq.${genomeSubset}`,
     `value.joint.freq.${jointSubset}`,
     'value.exome.filters',
+    'value.exome.fafmax',
     'value.genome.filters',
     'value.joint.filters',
     'value.alleles',