variablesets.sample-variant-stats-variableset.json Maven / Gradle / Ivy
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{
"uid": 0,
"id": "opencga_sample_variant_stats",
"name": "OpenCGA sample variant stats",
"unique": false,
"confidential": false,
"internal": true,
"description": "OpenCGA sample variant stats.",
"variables": [
{
"id": "id",
"name": "id",
"category": "",
"type": "STRING",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 0,
"dependsOn": null,
"description": "Sample identifier *",
"variables": null,
"attributes": null
},
{
"id": "variantCount",
"name": "variantCount",
"category": "",
"type": "INTEGER",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 1,
"dependsOn": null,
"description": "Number of variants where the sample has the main allele (i.e. 0/1, 1/1, ./1, 1/2, ...)",
"variables": null,
"attributes": null
},
{
"id": "chromosomeCount",
"name": "chromosomeCount",
"category": "",
"type": "MAP_INTEGER",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 2,
"dependsOn": null,
"description": "Number of variants per chromosome *",
"variables": null,
"attributes": null
},
{
"id": "typeCount",
"name": "typeCount",
"category": "",
"type": "MAP_INTEGER",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 3,
"dependsOn": null,
"description": "Variants count group by type. e.g. SNP, INDEL, MNP, SNV, ...",
"variables": null,
"attributes": null
},
{
"id": "genotypeCount",
"name": "genotypeCount",
"category": "",
"type": "MAP_INTEGER",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 4,
"dependsOn": null,
"description": "Number of variants per genotype. Only counts genotypes with the main allele. Phase is ignored. *",
"variables": null,
"attributes": null
},
{
"id": "indelLengthCount",
"name": "indelLengthCount",
"category": "",
"type": "MAP_INTEGER",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": [
"lt20",
"lt5",
"gte20",
"lt10",
"lt15"
],
"rank": 5,
"dependsOn": null,
"description": "Indel length grouped in ranges *",
"variables": null,
"attributes": null
},
{
"id": "filterCount",
"name": "filterCount",
"category": "",
"type": "MAP_INTEGER",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 6,
"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": "tiTvRatio",
"name": "tiTvRatio",
"category": "",
"type": "DOUBLE",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 7,
"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": 8,
"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": 9,
"dependsOn": null,
"description": "Standard Deviation of the quality",
"variables": null,
"attributes": null
},
{
"id": "heterozygosityRate",
"name": "heterozygosityRate",
"category": "",
"type": "DOUBLE",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 10,
"dependsOn": null,
"description": "Heterozygosity rate as defined by PLINK: (N–O)/N. . N is the number of non-missing genotypes. O is the observed number of homozygous genotypes for a given individual. ",
"variables": null,
"attributes": null
},
{
"id": "mendelianErrorCount",
"name": "mendelianErrorCount",
"category": "",
"type": "OBJECT",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 11,
"dependsOn": null,
"description": "Number of mendelian errors grouped by PLINK error codes grouped by Chromosome.",
"variables": null,
"attributes": null
},
{
"id": "consequenceTypeCount",
"name": "consequenceTypeCount",
"category": "",
"type": "MAP_INTEGER",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 12,
"dependsOn": null,
"description": "Variants count group by consequence type. e.g. missense_variant, synonymous_variant, stop_lost, .... Each counter is increased at most one per variant. If multiple overlapping transcripts have the same consequence type, it will count as one.",
"variables": null,
"attributes": null
},
{
"id": "biotypeCount",
"name": "biotypeCount",
"category": "",
"type": "MAP_INTEGER",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 13,
"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": "clinicalSignificanceCount",
"name": "clinicalSignificanceCount",
"category": "",
"type": "MAP_INTEGER",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": null,
"rank": 14,
"dependsOn": null,
"description": "Variants count group by clinical significance. e.g. benign, likely_benign, likely_pathogenic, pathogenic, uncertain_significance .... Each counter is increased at most one per variant. If multiple variant traits have the same clinical significance, it will count as one.",
"variables": null,
"attributes": null
},
{
"id": "depthCount",
"name": "depthCount",
"category": "",
"type": "MAP_INTEGER",
"defaultValue": null,
"required": false,
"multiValue": false,
"allowedValues": null,
"allowedKeys": [
"na",
"lt20",
"lt5",
"gte20",
"lt10",
"lt15"
],
"rank": 15,
"dependsOn": null,
"description": "Depth count",
"variables": null,
"attributes": null
}
],
"entities": [
"SAMPLE"
],
"release": 0,
"attributes": {
"avroClass": "class org.opencb.biodata.models.variant.metadata.SampleVariantStats"
}
}© 2015 - 2024 Weber Informatics LLC | Privacy Policy