LiftOver with zero-based UCSC chain file

Question

[Zhenyu Zhang]

I am planing to do some LiftOver from hg19 to 38. Well there is the tool and UCSC chain file. However, I roughly remember that UCSC uses zero-based coordinates, which is different from others. Will this create a problem? Should I edit ucsc chain file first by adding 1?

Answer 1

[Devon Ryan]

A given format always uses the same coordinate system. This will work perfectly fine as long as the chromosome names are compatible.

[Zhenyu Zhang]

So what you mean is that the effect of 0 vs 1 will cancel out, and I shouldn't be worried about it. Is that right?

[Devon Ryan]

No, what I mean is that there is no difference between UCSC and anything else. A format is a format, regardless of where it's from.

Edit: Perhaps I should mention that the tool itself has 0-based coordinates in mind.