Jobs

The main goal of the EVA pipeline is to store variants read from VCF files, calculate population statistics and annotate them using Ensembl's Variant Effect Predictor.

In order to do so, the following jobs are available:

Initializing the database (work in progress)
Processing a genotyped VCF
Processing an aggregated VCF
Re-annotating variants (work in progress)
Re-calculating statistics (work in progress)

Please note this section is a work in progress and more details about the structure of each job will be added in the future.

Initializing the database (work in progress)

It is not yet necessary to run this job in order to have a ready-to-use database. In the future, some preparation will be required for improved efficiency when querying the database.

This preparation will at least involve loading a feature set for the genome assembly the variation data is based on, to allow to translate from gene/transcript name to genomic coordinates.

Processing a genotyped VCF

One of the sources of data for the EVA ETL pipeline is a Variant Call Format (VCF) file listing the sample genotypes for each variant.

First, the alleles from columns REF and ALT are normalized to ensure that different representations across multiple VCFs will be recognized as the same. More information about the normalization process can be found in this presentation. Once normalized, variants are stored into the database.

Population statistics and annotation from Ensembl VEP can optionally be generated and stored along with the core variant information. These processes are shared across multiple jobs (VCF processing, re-annotation, etc) and will be documented separately.

Genotyped VCF job

Processing an aggregated VCF

One of the sources of data for the EVA ETL pipeline is a Variant Call Format (VCF) file not listing sample genotypes. Given that statistics such as allele frequencies can't be calculated based on the genotypes, they are often provided in the INFO column.

First, the alleles from columns REF and ALT are normalized to ensure that different representations across multiple VCFs will be recognized as the same. More information about the normalization process can be found in this presentation. Population statistics can be optionally read from the INFO column. Once both these steps are finished, variants are stored into the database.

Annotation from Ensembl VEP can optionally be generated and stored along with the core variant information. This process is shared across multiple jobs (VCF processing, re-annotation, etc) and will be documented separately.

Aggregated VCF job