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OpenCGA provides a set of analysis o compute basic statistics given a variant dataset. In order to get richer statistics, the variant data should comprise annotation and pedigree (samples, phenotypes,...).
OpenCGA computes three types of statistics:
Next sections describe the three types of statistics.
Summary or global stats provides significant information about the variant dataset. It includes:
- The total number of variants.
- The total number of samples.
- The number of variants per chromosome.
- The number of variants per consequence type.
- The number of variants per biotype.
- The number of variants per type (SNV, INDEL,...)
- The number of variants per genotype.
- The Ts/TV ratio or transition-to-transversion ratio.
- A heterozigosity score.
- A missingness score.
- A list of the most affected genes.
- Indel length
- A list of HPO and genes for loss of function (LoF) variants.
- A list of the most frequenct variant traits.
- The number of mendelian error per type of error.
- Relatedness scores (IBD/IBS scores).
Summary statistics are stored in a JSON format file.
Pre-calculated Variant 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
calculated for each variant, in addition, you may specify a set of samples (aka, cohort) in order to take into account only those samples.
VariantStats // Total number of alleles in called genotypes. Does not include missing alleles int alleleCount // Number of reference alleles found in this variant int refAlleleCount // Number of main alternate alleles found in this variant. Does 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
Variant stats include the following values:
- The total number of alleles (it does not include missing alleles)
- The number of reference alleles found in this variant
- The number of main alternate alleles found in this variant (it does not include secondary alternates)
- The reference allele frequency, i.e., the quotient of the number of reference alleles divided by the total number of alleles.
- The alternate allele frequency, i.e., the quotient of the number of alternate alleles divided by the total number of alleles.
- The number of occurrences for each genotype
- The frequency for each genotype
- The number of missing alleles
- The number of missing genotypes
- The minor allele frequency (maf)
- The minor genotype frequency (mgf)
- The allele with the minor frequency
- The genotype with the minor frequency
Pre-calculated stats are useful for filtering variants. This stats are intra-study, calculated within a given cohort.
Table of Contents:
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