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IGV displays genomic coordinates in a 1-based system or 0-based?

Could you please help me determine whether the Integrative Genomics Viewer (IGV) displays genomic coordinates in a 1-based or 0-based system? I have been unable to locate a reference page addressing this question. Your assistance would be greatly appreciated. Thank you.

integrative-genomics-viewer igv
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updated by ATpoint ATpoint • written by plusone • plusone

Thanks for your reply. I found one comment from it:

Fun fact regarding IGV: files with .igv ending are 0-based, while the IGV genome browser itself uses the 1-base to display sequences

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written by plusone • plusone

That was the comment I had linked in my comment above.

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written by GenoMax GenoMax

1 answer

These sorts of things are really easy to dig out. Open IGV, type into the Enter a gene or locus field chr1:0-10 and it will jump and display chr1:1-10, demonstrating it's 1-based which makes sense as 1-based is typically more intuituve for humans and as such suited for a GUI such as IGV.

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written by ATpoint ATpoint

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