LiftOver GRCh38 toGRCh37

Question

[davidjohngreen]

Hi all,

I have some variants from UKB exomes and need to convert them from GRCh38 to GRCh37 (to make the data compatible with some data I can't redo for several reasons). In LiftOver I can only find a chain file from GRCh38 to hg19, but I believe there are some differences (0 vs. 1 based numbering, different contig naming etc) that'll scupper my downstream analysis.

Is there a way to achieve this conversion robustly?

Many thanks in advance.

Answer 1

[LChart]

Just lift to hg19 and rename the contigs from "chr1" to "1" (etc.) The genomic content on the exomes will be identical.

what is the difference between GRCh37 and hg19 ?