Understanding the Notation of Genomic Variation Data

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6.5 years ago

bisansamara ▴ 20

I need help to understand following data:

    ref   alt
     *     1D, -G
     *     2D, -CT
     *     complex, +GG&-C
     *     complex, -G & K at 242795103
     *     -CTTC/*

So the full data has the chr# and positions of SNVs, in addition to the ref/alt nucleotide. Usually if the information of a nucleotide is not available, it’s written as “0”. And if it’s null, then it’s referred to as either “-“ or “.”

What does the “*” and “/” mean here? And how to re-write that so that the data could be annotated using ANNOVAR?

annovar variants annotation nucleotides mutations • 1.2k views

ADD COMMENT • link 6.5 years ago by bisansamara ▴ 20

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It is useful to provide origin of any data/annotation (software/site) that looks non-standard or does not follow established formats.

ADD REPLY • link 6.5 years ago by GenoMax 147k

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The data is from those two papers: (1) Science. 2012 Dec 21;338(6114):1619-22. DOI 10.1126/science Supplementary table 11 (2) Nature. 2012 Apr 4;485(7397):246-50. DOI 10.1038/nature10989 Supplementary table 3. Your help is much appreciated!

ADD REPLY • link 6.5 years ago by bisansamara ▴ 20

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