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Our Preferred Reference Sequence

You might remember Einstein telling you that there is no preferred inertial reference frame. So wrong that guy! ;) We definitely prefer GRCh37 for the human reference sequence! GRCh37 or hg19 is the latest build and its coordinate system is probably not going to change anymore. Updates are rather released as patches [1]. We therefore use GRCh37 for our reference sequence by default.

If you prepared your vcf file properly, the reference used is noted in the header (e.g. ##reference=hg19). GeneTalk checks if your vcf is compatible with GeneTalk. If it is not, GeneTalk will give warning and you can run a proper coordinate transversion to hg19/GRChr37 (e.g. with the UCSC liftover tool [2]) before uploading your vcf file.

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