liftover output column help

Question

[amy__]

Hello,

When I input this (just a section of the whole file) hg19 location to hg38

chr1    45794129    45796519

liftover outputs this

chr1    45328457    45330847    chr1:45794130-45796519  1

What is the 4th column and why is it outputted?

Thanks! Amy

Answer 1

[Pierre Lindenbaum]

chr1 45328457 45330847 chr1:45794130-45796519 1

What is the 4th column and why is it outputted?

the fourth column is a reminder of your original input (chr1 45794129 45796519 = 0-Based BED interval) as a 1-Based interval (CHR):(START+1):(END)

see also: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems

[amy__]

Amazing, thank you!

[Pierre Lindenbaum]

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