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:

• Summary

  Variant stats

• Sample stats
• Variant Cohort stats
• Family stats

Next sections describe the three types of these statistics.

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variant

variant

Summary statistics are stored in a JSON format file.

AnchorvariantvariantVariant 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.

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.