Tutorial:Coordinate Systems and genomic variant description
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10 months ago
Juke34 8.6k

Once in a while I'm struggling with coordinate systems, so I end up googling for it and most of time I find the nice post made by Obi Griffith. Time to time I find other very interesting ressources. The subject is very well documented but some information are scattered over different posts and/or blogs. This time I took the time to read and collect the information and tried to synthetise in one place (a GitHub repo). I know, it is an umpteenth place that will talk about the subject... but at least it is useful to me. Hoping it might be useful to others too.

Here is the address: https://juke34.github.io/coordinate_systems/

coordinate-system HGVS normalization VCF • 666 views
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I find Pierre's comment on that post really insightful: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems

people use an API to read the BAM data. For example htsjdk/SAMRecord.getAlignmentStart() returns the 1-based POS

In other words, you'll never have to consider BAM's coordinate system unless you're writing a BAM parser.

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