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GEMINI annotate (version 0.20.1+galaxy2)
Only files with version 0.20.1 are accepted.
The tool can use the information from a BED or VCF dataset to annotate the database variants.
The default is to consider VCF-formatted annotations only if a variant in the GEMINI database and a record in the annotation source describe the exact same nucleotide change at the same position in the genome. You can disable this option to make use of any annotation that overlaps with the position of a database variant. This setting is ignored for annotation sources in BED format, for which matching is always based on overlapping positions only.
Annotation extraction recipes
Annotation extraction recipe 0

What it does

Given an existing GEMINI database and an annotation source in BED or VCF format, the annotate tool will, for each variant in the variants table of the database, screen for overlapping regions defined in the annotation source and update one or more new columns of the variant record in the database based on the result and the annotation found.