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GEMINI query (version 0.10.1.0)

GEMINI database:

Only files with version 0.10.1 are accepted.

The query to be issued to the database:

(-q)

Restrictions to apply to genotype values:

(--gt-filer)

SQL filter to use to filter the sample table:

(--sample-filter)

Add a column of all sample names with a variant to each variant:

(--show-samples)

Add a column listing all of the families with a variant to each variant:

(--show-families)

Perform the sample-filter on a family-wise basis:

(--family-wise)

Add a header of column names to the output:

(--header)

Minimum number of families for a variant passing a family-wise filter to be in:

-1 means default values (--min-kindreds)

Request drug-gene interaction info from DGIdb:

(--dgidb)

A variant must be in either all, none or any samples passing the sample-query filter:

(--in)

Restrict query to this region:

e.g. chr1:10-20 (--region)

What it does

The real power in the GEMINI framework lies in the fact that all of your genetic variants have been stored in a convenient database in the context of a wealth of genome annotations that facilitate variant interpretation. The expressive power of SQL allows one to pose intricate questions of one’s variation data. This tool offers you an easy way to query your variants!

http://gemini.readthedocs.org/en/latest/content/querying.html

Citation

If you use GEMINI in your research, please cite the following manuscript: