variablesets.cohort-variant-stats-variableset.json Maven / Gradle / Ivy

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{
  "uid": 0,
  "id": "opencga_cohort_variant_stats",
  "name": "OpenCGA cohort variant stats",
  "unique": true,
  "internal": false,
  "confidential": false,
  "description": "OpenCGA cohort variant stats.",
  "variables": [
    {
      "id": "variantCount",
      "name": "variantCount",
      "category": "",
      "type": "INTEGER",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 0,
      "dependsOn": null,
      "description": "Number of variants in the variant set",
      "variables": null,
      "attributes": null
    },
    {
      "id": "sampleCount",
      "name": "sampleCount",
      "category": "",
      "type": "INTEGER",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 1,
      "dependsOn": null,
      "description": "Number of samples in the variant set",
      "variables": null,
      "attributes": null
    },
    {
      "id": "filterCount",
      "name": "filterCount",
      "category": "",
      "type": "MAP_INTEGER",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 2,
      "dependsOn": null,
      "description": "The number of occurrences for each FILTER value in files from this set..  Each file can contain more than one filter value (usually separated by ';').. ",
      "variables": null,
      "attributes": null
    },
    {
      "id" : "genotypeCount",
      "name" : "genotypeCount",
      "category" : "",
      "type" : "MAP_INTEGER",
      "defaultValue" : null,
      "required" : false,
      "multiValue" : false,
      "allowedValues" : null,
      "allowedKeys" : null,
      "rank" : 3,
      "dependsOn" : null,
      "description" : "Number of genotypes found for all samples in variants set",
      "variableSet" : null,
      "variables" : null,
      "attributes" : null
    },
    {
      "id": "filesCount",
      "name": "filesCount",
      "category": "",
      "type": "INTEGER",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 4,
      "dependsOn": null,
      "description": "Number of files in the variant set",
      "variables": null,
      "attributes": null
    },
    {
      "id": "tiTvRatio",
      "name": "tiTvRatio",
      "category": "",
      "type": "DOUBLE",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 5,
      "dependsOn": null,
      "description": "TiTvRatio = num. transitions / num. transversions",
      "variables": null,
      "attributes": null
    },
    {
      "id": "qualityAvg",
      "name": "qualityAvg",
      "category": "",
      "type": "DOUBLE",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 6,
      "dependsOn": null,
      "description": "Mean Quality for all the variants with quality",
      "variables": null,
      "attributes": null
    },
    {
      "id": "qualityStdDev",
      "name": "qualityStdDev",
      "category": "",
      "type": "DOUBLE",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 7,
      "dependsOn": null,
      "description": "Standard Deviation of the quality",
      "variables": null,
      "attributes": null
    },
    {
      "id": "typeCount",
      "name": "typeCount",
      "category": "",
      "type": "MAP_INTEGER",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 8,
      "dependsOn": null,
      "description": "Variants count group by type. e.g. SNP, INDEL, MNP, SNV, ...",
      "variables": null,
      "attributes": null
    },
    {
      "id": "biotypeCount",
      "name": "biotypeCount",
      "category": "",
      "type": "MAP_INTEGER",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 9,
      "dependsOn": null,
      "description": "Variants count group by biotype. e.g. protein-coding, miRNA, lncRNA, ....  Each counter is increased at most one per variant. If multiple overlapping genes have the same biotypes, it will count as one.",
      "variables": null,
      "attributes": null
    },
    {
      "id": "consequenceTypeCount",
      "name": "consequenceTypeCount",
      "category": "",
      "type": "MAP_INTEGER",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 10,
      "dependsOn": null,
      "description": "Variants count group by consequence type. e.g. synonymous_variant, missense_variant, stop_lost, ...",
      "variables": null,
      "attributes": null
    },
    {
      "id": "chromosomeCount",
      "name": "chromosomeCount",
      "category": "",
      "type": "MAP_INTEGER",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 11,
      "dependsOn": null,
      "description": "Number of variants per chromosome",
      "variables": null,
      "attributes": null
    },
    {
      "id": "chromosomeDensity",
      "name": "chromosomeDensity",
      "category": "",
      "type": "MAP_DOUBLE",
      "defaultValue": null,
      "required": false,
      "multiValue": false,
      "allowedValues": null,
      "allowedKeys": null,
      "rank": 12,
      "dependsOn": null,
      "description": "Total density of variants within the chromosome. counts / chromosome.length",
      "variables": null,
      "attributes": null
    }
  ],
  "entities": [
    "COHORT"
  ],
  "release": 0,
  "attributes": {
    "avroClass": "class org.opencb.biodata.models.variant.metadata.VariantSetStats"
  }
}