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Pre-calculated stats are useful for filtering variants. This stats are intra-study, calculated within a given cohort.
Cohorts are defined as a arbitrary group of samples. Cohorts can be defined in Catalog, either selecting samples one by one or selecting all samples that share some attributes like population or phenotype.
If a cohort is modified after calculating the statistics, the existing statistics became INVALID.
By default, in each study, there is defined the cohort ALL that contains all the samples loaded in the study. Every time that new samples are loaded in the study, this cohort is modified, and the statistics have to be recomputed.
There are two types of statistics, per variant, and global statistics. Variant statistics are stored in the variants database, within the StudyEntry. Global statistics are stored in Catalog.
Variant Stats (intra variant)
These stats are calculated for each variant, and for a set of samples (cohort).
Code Block title Result
VariantStats // Total number of alleles in called genotypes. DoDoes not include missing alleles int alleleCount // Number of reference alleles found in this variantsvariant int refAlleleCount // Number of main alternate alleles found in this variantsvariant. DoDoes not include secondary alternates int altAlleleCount // Reference allele frequency calculated from refAlleleCount and alleleCount, in the range (0,1) float refAlleleFreq // Alternate allele frequency calculated from altAlleleCount and alleleCount, in the range (0,1) float altAlleleFreq // Count for each genotype found map<int> genotypeCount // Genotype frequency for each genotype found map<float> genotypeFreq // Number of missing alleles int missingAlleleCount // Number of missing genotypes int missingGenotypeCount // Minor allele frequency float maf // Minor genotype frequency float mgf // Allele with minor frequency string mafAllele // Genotype with minor frequency string mgfGenotype
Usually, public studies do not provide samples data. In this situations is not possible to calculate the statistics. Instead, the statistics can be extracted from the INFO column. Unfortunately, there is no standard way for defining multi-cohort statistics in the VCF format. Instead, OpenCGA recognizes three different formats for representing statistics.
- BASIC mode
- EVS mode
- EXAC mode
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