Understanding the Notation of Genomic Variation Data
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3.4 years ago
bisansamara ▴ 10

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?

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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.

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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!