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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 stats

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.

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.

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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