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Variant Stats contain a basic information for each variant in a different cohort.
Implementation
Variant Stats is implemented using Hadoop MapReduce over HBase.
Input
Parameters
OpenCGA support different input parameters:
- Variant Query
- Sample list, cohort or query
Output
Files
Variant stat file including the following values:
If the stats are not indexed, the analysis produces a Variant stats file with the following model schema:
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Index
Pre-computed stats are useful for filtering variants. This stats are intra-study, calculated within a given cohort.
Useful Links
Table of Contents:
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