3 posts
A practical guide to moving variants, intervals, and gene models between GRCh37, GRCh38, and T2T-CHM13 using chain-based liftover, Liftoff, and LiftOn, with checks that tell you when the result is wrong.
hg19 is UCSC's packaging of the GRCh37 human reference assembly. They are nearly the same sequence with different chromosome names and a different mitochondrion, and the coordinates do not match GRCh38. Here is how to tell which build your files use and how to move between them without corrupting your data.
A working guide to lifting positions, VCFs, intervals, and probe manifests between GRCh37, GRCh38, and T2T-CHM13, including which tool to use for each file type and how to tell when the lift silently went wrong.