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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:
Summary statistics are stored in a JSON format file.
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:
Pre-calculated stats are useful for filtering variants. This stats are intra-study, calculated within a given cohort.
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