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

If the stats are not indexed, the analysis produces a Variant stats file in json format with the following model schema:

Variant Stats Data Mode

Index

Pre-computed stats are useful for filtering variants. This stats are intra-study, calculated within a given cohort.

Useful Links

Table of Contents: