LiftOver GRCh38 toGRCh37 · Biostar

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LiftOver GRCh38 toGRCh37

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.

liftover

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updated 3.8 years ago by LChart

• written 3.8 years ago by davidjohngreen •

1 answer

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 ?

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written 3.8 years ago by LChart

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