The Privacy Tool extracts the genotype(s) from the VCF/CGI files and implants clinically associated variants into the list of transmitted variants. For the clinically associated variants we used UCSC table named Flagged SNPs132. The Privacy Tool accepts VCF files. Download the Privacy Tool. Questions, Comments, Suggestions? Post on Biostar.
A deidentified file ready for SG ADVISER annotation will be *Your Filename*.Deidentified.tar.gz. To annotate this file you can proceed to genomics.scripps.edu and upload the file for annotation.
Identification strips the clinically associated variants previously implanted and imports back the genotype(s). For identification please import the SG ADVISER annotated file then from the tool folder select the *filename*.Identified file. The final annotated and identified file will be final_*filename*.Identified. You can import this file into the SG ADVISER UI for sorting and filtering.
NOTE: depending of the file(s) size both process can take a long time (up to 10 minutes). Please be patient and wait for a notification that deidentification/ identification has finished and you see the output files in the tool's folder.