Omics Analytics
Omics Analytics stores provide a centralized repository for genetic and genomic data, making it easier to manage and analyze large volumes of data. Analytics stores must be listed as “Active” before they are made ready to ingest data. Once the data is ingested, you can also view and query your data in Amorphic Query Engine. In Amorphic we have two types of analytics storage.
Variant Store
A Variant store is a data store that stores variant data at a population scale. Variant store helps to collect genomic objects, specifically variant call formats files (VCFs), which function as a genomic file. Variant stores support both gVCF and VCF inputs.
Annotation Store
An annotation store is a data store that holds annotation data and holds information about variants, genes, or genomic regions of interest. Annotation stores support storage of files in TSV/CSV, VCF, and GFF formats.
To use Omics Analytics, HCLS should be enabled in the environment.
How to Create an Analytics Store
You can create new analytics store by clicking + New Store button in Omics Analytics page and filling required information. The analytics store creation is an asynchronous process hence you need to wait till the store becomes active before you start importing jobs.
Below image show how to create a new Omics Analytics Store
To create a new analytics store, either input the details shown in the table below or directly upload the JSON data.
Metadata
| Properties | Details |
|---|---|
| Store Name | Store name must start with an alphabet and can only contain 3-254 alphanumeric & _ characters only, and must be unique. |
| Store Type | Type of analytics store - Omics Variant/Omics Annotation. |
| Description | Description of the store being created. |
| Keywords | Keywords indexed & searchable in app. Choose meaningful keywords to flag related stores & easily find them later. |
Store Configurations
| Store Configs | Details |
|---|---|
| Reference Store | Reference Store name that you previously created where your reference genome is. |
| Reference Genome | The genome reference for the store's annotations from list of references in the Reference Store. |
| Data File Format | The annotation file format of the store. It can be either VCF, GFF or TSV. This option is only for Annotation store. |
| Schema Definition | The schema which describes column names and type of your annotation file. The schema must be defined when the Data File Format TSV. |
Import Jobs
Import job is the process of importing genomic data into Analytics Store that you created for analysis.
To start an import job you need a dataset which contains your genomic data. Each store only supports import of data files of format that you chose during the creation of the analytics store.
Omics Variant stores can ingest files in gVCF and VCF formats. Where as Annotation Store support either TSV/CSV, VCF, or GFF files. The store must be in active state before you can start an import job and all data imported in an Analytics Store must be in the same format.
Below image show how to start and import job
To start an import job in Analytics Store following details are required
Import Job Configurations
| Properties | Details |
|---|---|
| Dataset Id | The dataset where you genome file that you want to import resides. |
| Job Name | The name of your import job. |
| Description | Description of the import job. |
| File Name | The filename of genome data file that you want to import from the selected dataset. |
Import job is an asynchronous process and once the import of data is completed, you can view and query the data from Amorphic Query Engine present under the domain of your Analytics Store name.
Delete Analytics store
You can delete an Analytics Store by clicking the 'dustbin' icon in store details page.
Deletion of Analytics Store is an asynchronous process. Once you delete an Analytics Store it is a permanent delete operation and all the associated domains, datasets and import jobs are deleted along with it.
Below image show how to delete an Analytics Store
