Vcf Database Table Structure

Question

[win]

hi all, I am trying to store VCF files in a database table. While the VCF file structure is quite straight forward the issue I am thinking about is when one has more than sample in the VCF file.

Does anyone have any recommendations for relational table structure to store VCF file.

thanks in advance.

[Pierre Lindenbaum]

related :

Which type of database systems are more appropriate for storing information extracted from VCF files

Do people import VCF files into databases?

Answer 1

[Pierre Lindenbaum]

I use that kind of schema: (http://code.google.com/p/variationtoolkit/wiki/Vcf2Sqlite)

But I've never really used it . Why ? New ideas, new tools, new sources of annotations: I often re-annotate my VCF file . It's easier to parse some tabix-indexed files rather than storing them in a database.

[win]

thanks, i will probably try sqlite.

Answer 2

[User 59]

Have a look at Gemini:

Code: http://github.com/arq5x/gemini

Docs: https://gemini.readthedocs.org/en/latest/index.html

Blurb:

Gemini is designed to be a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes, and useful genome annotations into an integrated database framework, gemini provides a simple, flexible, yet very powerful system for exploring genetic variation for for disease and population genetics.