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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:
 Summary
 Sample stats
 Variant Cohort stats
 Family stats
Next sections describe the three types of statistics.
AnchorsummarysummarySummary statsSummary 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 transitiontotransversion 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 filethese statistics.
Anchor  


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
Precalculated stats are useful for filtering variants. This stats are intrastudy, calculated within a given cohort.
Anchor  


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 Ts/TV ratio or transitiontotransversion 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.
Table of Contents:
Table of Contents  

