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Overview

The main goal for indexing variant data into OpenCGA Storage is to be able to make queries and extract this data in a efficient way. There are different alternatives ways to access to the data (via CLI, RESTful , Java API, Python API, ...) and multiple implementations of the VariantStorageManager (OpenCGA Storage MongoDB, OpenCGA Storage Hadoop, ...).

All this layers and implementations will use the same specification defined in this document.

There are defined an small set of READ-ONLY methods to achieve all the required functionality.

• Query Return all variants that matches with a given query
• Count Count the result of a given query
• GroupBy & Rank Group variants by some field and, optionally, creates a rank by number of variants.
• Frequency Group variants by region and count. Useful to plot histograms.

Query filters

A filter is a pair of <key>, <value>, where the keys are predefined, and the values are defined by the user, using an specific format. In the next sections, all this keys are going to be enumerated, explaining their effect and the required format of the value.

There are some general rules that are applied for every case:

1. Returned variants will match positively with all the filters, except with the positional filters. Variants will need to match with, at least, one positional filter (if any).

2. When a filter accepts a list of values, they can be separated with:

   • Comma , : Which will define an OR operation between the separated elements
   • Semicolon ; : Which will define an AND operation between the separated elements

So, the query chromosome: 2,3 will return all variants with 2 and 3, but chromosome: 2;3 will return all variants in chromosomes 2 and 3, but chromosome: 2;3 will return an empty result, because there are no variants in chromosomes 2 and 3 at the same time.

General filters

This general filters will match with fields from the VCF input files.

All this parameters are positive filters. The output will contain variants that match with this filters.

Statistics filters

Apart from the data provided on the files, there are some statistics calculated from the genotypes, or parsed from the INFO column, if the input was an aggregated file.

This filters are related with the statistics from a specific study and cohort. Knowing that, the format will be the same for each filter: <study>:<cohort><comparator><value>, where the available comparators are: <, <=, >, >=, = and !=.

Annotation filters

Modifiers

Modifies over the variants to return.

Variant Fields

The parameters include and exclude accepts a list of Variant Fields. This is a list with all the accepted values. Some short alias to those fields are listed in italic.

• id
• chromosome
• start
• end
• reference
• alternate
• length
• type
• studies

  • studies.samplesData | samples | samplesData

  • studies.files | files

  • studies.stats | stats

  • studies.secondaryAlternates

  • studies.studyId

• annotation
  • annotation.ancestralAllele
  • annotation.id
  • annotation.xrefs
  • annotation.hgvs
  • annotation.displayConsequenceType
  • annotation.consequenceTypes
  • annotation.populationFrequencies
  • annotation.minorAllele
  • annotation.minorAlleleFreq
  • annotation.conservation
  • annotation.geneExpression
  • annotation.geneTraitAssociation
  • annotation.geneDrugInteraction
  • annotation.variantTraitAssociation
  • annotation.functionalScore
  • annotation.additionalAttributes

GroupBy and Rank

Histogram