Add heterozygous skewed allele count to VA

broadinstitute · Aug 14, 2024 · 0ec7af6 · 0ec7af6
1 parent 0e86c17
commit 0ec7af6
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Showing 2 changed files with 26 additions and 2 deletions.
diff --git a/graphql-api/src/graphql/resolvers/va.spec.ts b/graphql-api/src/graphql/resolvers/va.spec.ts
@@ -59,6 +59,11 @@ describe('resolveVACohortAlleleFrequency', () => {
     faf95: { popmax: 0.123, popmax_population: 'afr' },
     ancestry_groups: [],
     filters: ['AC0'],
+    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 variantESDocument = {
@@ -103,7 +108,7 @@ describe('resolveVACohortAlleleFrequency', () => {
           lowComplexityRegion: true,
           lowConfidenceLossOfFunctionError: true,
           lossOfFunctionWarning: true,
-          heterozygousSkewedAlleleCount: null,
+          heterozygousSkewedAlleleCount: 37,
         },
       },
     ]

diff --git a/graphql-api/src/graphql/resolvers/va.ts b/graphql-api/src/graphql/resolvers/va.ts
@@ -371,6 +371,25 @@ 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]
+}
+
 export const resolveVACohortAlleleFrequencies = async (
   obj: any,
   args: any,
@@ -393,7 +412,7 @@ export 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 = {