# Overview Your Genomic Data Analysis Suite ## Home An integrated suite of high-performance (big data) applications for the management and analysis of population-scale genomic data. ![OpenCB Summary](http://docs.opencb.org/download/thumbnails/327710/image2020-8-13_18-25-38.png?version=1\&modificationDate=1597335938379\&api=v2) **By replacing datafiles with databases our software promotes:** * Scalability; the ability to run queries in real-time across hundreds of thousands of genomes. * Accessibility; the ability to analyse from anywhere on the web without needing access to the local filesystem. * Integration; the ability to link data together using flexible data models covering reference data, variant data and clinical metadata. * Security; the ability to protect data using federated (e.g. SSO) authentication and role-based authorisation schemes. **OpenCB solutions are typically used as:** * The storage target of secondary analysis pipelines. * The data source for tertiary analysis workflows. **The open-source OpenCB software is developed and maintained by researchers from multiple organisations and made freely available at** \*\*\*\* \*\*\*\* Becoming a super hero is a fairly straight forward process: ``` $ give me super-powers ``` {% hint style="info" %} Super-powers are granted randomly so please submit an issue if you're not happy with yours. {% endhint %} Once you're strong enough, save the world: {% code title="hello.sh" %} ```bash # Ain't no code for that yet, sorry echo 'You got to trust me on this, I saved the world' ``` {% endcode %} # News s # My Hello START INCLUDE - 3 END INCLUDE @author: Jacobo # OpenCGA ## Overview bla bla ## Variant query `GET` `opencga/v1/variant/query` This methods query variants #### Path Parameters | Name | Type | Description | | ---- | ------ | ----------- | | | string | | {% tabs %} {% tab title="200 " %} ``` ``` {% endtab %} {% endtabs %} # CellBase ## Overview ... # IVA # Variant # Variant Data Model |

id

String

| Unique variant ID, this consists of chromosome, position, reference and alternate alleles in this format: *chrom:pos:ref:alt* | | ---------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | |

names

List\

| Other IDs found for this genomic variant across all VCF files indexed | |

chromosome

String

| The chromosome where the genomic variant is located | |

start

int

| The 1-based position where the genomic variant starts. For variants coming from VCF files, this position is likely to be normalised, in this case, the original call in the file is stored in *studies.files.call* (see below) | |

end

int

| The 1-based position where the genomic variant ends. For variants coming from VCF files, this position is likely to be normalised, in this case, the original call in the file is stored in *studies.files.call* (see below) | |

reference

String

| Reference allele. For variants coming from VCF files, this position is likely to be normalised, in this case, the original call in the file is stored in *studies.files.call* (see below) | |

alternate

String

| Alternate allele. For variants coming from VCF files, this position is likely to be normalised, in this case, the original call in the file is stored in *studies.files.call* (see below) | |

strand

String

| Reference strand for this variant, by default all variants are represented in the positive strand | |

length

int

| Length of the genomic variation which depends on the variant type | |

type

VariantType

| Type of variant, the accepted types and Sequence Ontology (SO) terms are: | |

sv

StructuralVariation

| Specific information for Structural Variants | |

studies

List\

| Information specific to each study the variant was read from, such as samples or statistics | | **annotatio** | | # Release Notes ## 15.0.0 - 2042-12-03 ### Fixed * Removed humans, they weren't doing fine with animals. ### Changed * Animals are now super cute, all of them. ## 14.0.0 - 2042-10-06 ### Added * Introduced animals into the world, we believe they're going to be a neat addition. # Contributors ## Active ... ... ## Former Contributors ... ... # FAQ ## Can I become who I want to be? That's a tough question but thankfully, our team is on it. Please bear with us while we're investigating. ## Have you had a chance to answer the previous question? Yes, after a few months we finally found the answer. Sadly, Mike is on vacations right now so I'm afraid we are not able to provide the answer at this point. ## asdf # Users Users of OpenCB These are the users of OpenCB * Genomics England * NIHR