The nightmare of coordinate systems

Question

[Ana]

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?

Answer 1

[Pierre Lindenbaum]

Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems

Answer 2

[tomas4482]

https://tidyomics.com/blog/2018/12/09/2018-12-09-the-devil-0-and-1-coordinate-system-in-genomics/

https://genome-blog.soe.ucsc.edu/blog/2016/12/12/the-ucsc-genome-browser-coordinate-counting-systems/

Answer 3

[cmdcolin]

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

Answer 4

[Juke34]

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