Variant Stats

Pre-calculated stats are useful for filtering variants. This stats are intra-study, calculated within a given cohort.

Cohorts

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.

Stats models

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.

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:

• Variant stats

• Sample stats
• Cohort stats
• Family stats

Next sections describe these statistics.

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variant variant

Variant stats

Variant stats are 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

Aggregated statistics

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.

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.

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summary summary

Sample stats

Sample stats are calculated for each sample. It includes the following information:

• The total number of variants.
• 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 transition-to-transversion ratio (ti/tv ratio).
• A heterozigosity score.
• A missingness score.
• A list of the most affected genes.
• The number of variants per indel length
• A list of HPO and genes for loss of function (LoF) variants.
• A list of the most frequent variant traits.

Summary statistics are stored in a JSON format file.