The nightmare of coordinate systems
4
2
Entering edit mode
21 months ago
Ana ▴ 20

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?

one-based zero-based lef-aligned right-aligned • 1.1k views
ADD COMMENT
2
Entering edit mode
21 months ago
cmdcolin ★ 3.8k

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

ADD COMMENT
0
Entering edit mode
8 months ago
Juke34 8.5k

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

ADD COMMENT

Login before adding your answer.

Traffic: 1436 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6