Genomic NGS Tool
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Genomics import package for users  Package containing plugin jar, Sequence Ontology metadata files, data files and User's guide for running the Genomics import tool within version 1.7 of the i2b2 workbench.  This software converts output from VCF, ANNOVAR or GVF to I2B2 observation_fact format.  Perl scripts are used to convert files to GVF; the import tool software converts GVF to I2B2 facts described by Sequence Ontology concepts and modifiers.  Software source files can be downloaded from GitHub:

The Perl scripts are additionally provided here for convenience: