Add heterozygous skewed allele count to VA

Author: phildarnowsky-broad

graphql-api/src/graphql/resolvers/va.spec.ts

@@ -61,6 +61,11 @@ describe('resolveVACohortAlleleFrequency', () => {
     ancestry_groups: [],
     filters: ['AC0'],
     flags: ['monoallelic'],
+    quality_metrics: {
+      allele_balance: {
+        alt: { bin_freq: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] },
+      },
+    },
   }
 
   const genomeEsDocument = {
@@ -72,6 +77,16 @@ describe('resolveVACohortAlleleFrequency', () => {
     filters: ['AC0'],
     ancestry_groups: [],
     flags: ['monoallelic'],
+    quality_metrics: {
+      allele_balance: {
+        alt: {
+          bin_freq: [
+            100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116,
+            117, 118, 119,
+          ],
+        },
+      },
+    },
   }
 
   const variantESDocument = {
@@ -117,7 +132,7 @@ describe('resolveVACohortAlleleFrequency', () => {
           lowComplexityRegion: true,
           lowConfidenceLossOfFunctionError: true,
           lossOfFunctionWarning: true,
-          heterozygousSkewedAlleleCount: null,
+          heterozygousSkewedAlleleCount: 37,
         },
       },
     ]
@@ -158,7 +173,7 @@ describe('resolveVACohortAlleleFrequency', () => {
           lowComplexityRegion: true,
           lowConfidenceLossOfFunctionError: true,
           lossOfFunctionWarning: true,
-          heterozygousSkewedAlleleCount: null,
+          heterozygousSkewedAlleleCount: 237,
         },
       },
     ]

graphql-api/src/graphql/resolvers/va.ts

@@ -381,6 +381,25 @@ const addSubcohorts = (
   return Object.values(subcohortMap)
 }
 
+type ESFrequencies = {
+  quality_metrics: {
+    allele_balance: {
+      alt?: {
+        bin_freq: number[]
+      }
+    }
+  }
+}
+
+const calculateHeterozygousSkewedAlleleCount = (frequencies: ESFrequencies): number | null => {
+  const { alt } = frequencies.quality_metrics.allele_balance
+  if (!alt) {
+    return null
+  }
+
+  return alt.bin_freq[18] + alt.bin_freq[19]
+}
+
 const resolveVACohortAlleleFrequencies = async (
   obj: any,
   args: any,
@@ -406,7 +425,7 @@ const resolveVACohortAlleleFrequencies = async (
     lowComplexityRegion: obj.flags.includes('lcr'),
     lowConfidenceLossOfFunctionError: obj.flags.includes('lc_lof'),
     lossOfFunctionWarning: obj.flags.includes('lof_flag'),
-    heterozygousSkewedAlleleCount: null,
+    heterozygousSkewedAlleleCount: calculateHeterozygousSkewedAlleleCount(frequencies),
   }
 
   const fullSet: Subset = {