Shared flows
This section illustrates sequences of steps that are shared by multiple jobs.
The following flows are currently defined:
- Generate VEP annotation
- Calculate population statistics (work in progress)
Please note this section is a work in progress and more details about the structure of each flow will be added in the future.
Variant annotations are generated using Ensembl VEP, a binary completely independent from the EVA pipeline. In fact, one could annotate each study with a different version of VEP.
In order to annotate variants that have been previously loaded, the database is traversed, looking for those lacking an annotation. The output of this is a tab-separated file following the format described here.
In addition to this tab-separated file, the following are also necessary to run VEP:
- A FASTA file containing the sequence matched by the VCF
- A VEP cache containing transcripts location, regulatory regions, SIFT/Polyphen scores, etc.
FASTA files and VEP caches ready to be used together can be found in the Ensembl FTP, here and here.
VEP creates a plain text file with the annotations, which is then read and loaded into the database along with the variants.
(Click on the diagram for fullscreen view)
TODO