update CAF JSON

ga4gh · Oct 20, 2023 · 315e49f · 315e49f
1 parent af5b573
commit 315e49f
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Showing 2 changed files with 22 additions and 4 deletions.
diff --git a/schema/Makefile b/schema/Makefile
@@ -3,7 +3,7 @@
 .SUFFIXES:
 .DELETE_ON_ERROR:
 
-JSYAMLS:=annotation.yaml varstatement.yaml
+JSYAMLS:=annotation.yaml varstatement.yaml cohortAlleleFreq.yaml
 JSONS:=${JSYAMLS:.yaml=.json}
 
 all: ${JSONS} defs

diff --git a/schema/cohortAlleleFreq.json b/schema/cohortAlleleFreq.json
@@ -343,11 +343,29 @@
             "homozygotes": {
                "type": "integer"
             },
-            "meanDepth": {
-               "type": "number"
+            "hemizygotes": {
+               "type": "integer"
             }
          },
-         "additonalProperties": false
+         "additionalProperties": false
+      },
+      "qualityMeasures": {
+         "meanDepth": {
+            "type": "number"
+         },
+         "qcFilters": {
+            "type": "array",
+            "items": {
+               "type": "string"
+            }
+         },
+         "lowComplexityRegion": {
+            "type": "boolean"
+         },
+         "heterozygousSkewedAlleleCount": {
+            "description": "The count of individuals called as heterozygous for this variant with a skewed allele balance, indicating some of these individuals may be miscalled homozygous alternative allele.",
+            "type": "integer"
+         }
       },
       "subcohortFrequency": {
          "type": "array",