I am trying to lift over from build 38 to build 37, and here is my code: rg37 = hl.get_reference('GRCh37') rg38 = hl.get_reference('GRCh38') rg38.add_liftover("/hail_resources/grch37_to_grch38.over.chain.gz", rg37) mt = mt.annotate_rows(new_locus=hl.liftover(mt.locus, 'GRCh37')) mt = mt.filt…

Hey @genome , Can you include the full stack trace? GL000199.1 is indeed a valid GRCh37 contig. It appears that either: Hail has a bug. Maybe your matrix table actually contains GRCh37 loci and this error indicates that we did not expect GRCh37 loci in a GRCh38 Matrix Table?

I got this figured out, thank you!

@genome I have the same error. What was the solution? Thanks.

@igorm , if you run mt._force_count_rows() before the liftover, does that raise an error?

The chain file work very well for me rg38.add_liftover(“/hail_resources/grch38_to_grch37.over.chain.gz”, rg37)

Liftover from 38 to 37

Hail Query & hailctl

hanl1 January 24, 2023, 9:22pm 6

(post deleted by author)

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Liftover from 38 to 37

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