I am trying to clarify the different coordinate systems used to represent variants in the different platforms or standards. I have identified different systems such as left alignment, right alignment, fully alignment, zero-based, one-based... Nevertheless, I cannot fully understand the difference between right/left alignment and 0/1 based coordinates. Is there any difference? Are they synonyms?
4 answers
other answers are good for 0 vs 1 based coordinates, but you mentioned left and right alignment which may refer to "variant normalization" https://genome.sph.umich.edu/wiki/Variant_Normalization
There is this excellent presentation from Bob Milius, which talk about the problem with variants (from page 12) http://17ihiw.org/wp-content/uploads/2016/10/20160925_SequenceCoordinates_ASHI2016.pdf
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