Dear Hail team: I’m wondering if it is possible to liftover a table from GRCH37 to GRCH38? I realized there is a function to liftover a locus, but can I liftover an entire hail table? Thanks! Best regards, Wei

Konrad is planning to add a bit about this in the how-to, but here’s his example: Lift over the locus coordinates in a Table or MatrixTable from reference genome 'GRCh37' to 'GRCh38': >>> rg37 = hl.get_reference('GRCh37') # doctest: +SKIP >>> rg38 = hl.get_reference('GRCh38') # doctest…

Hi Tim, Thank you very much! That solves the problem. Best regards, Wei

Hi Tim, Can I follow up with a related question? I successfully lifted over an hail table using your code. Now I want to annotate a MatrixTable using this Table with the following command: mt = mt.annotate_rows(gnomAD = gn[mt.locus, mt.alleles]) But I got the following error message. My suspici…

this error (137) is usually a Spark out-of-memory exception. The code you’re running seems perfectly fine. What kind of cluster are you running on?

Thanks for your reply! I’m using a 24-node cluster from AWS, with 192 VCores and 576 Gb memory.

what is the full pipeline you are running?

Load data mt = hl.read_matrix_table(‘all.SNVs.vqsr.mt’) gnomAD annots gn = hl.read_table(‘gnomad.genomes.r2.1.sites.ht’) rg37 = hl.get_reference(‘GRCh37’) rg38 = hl.get_reference(‘GRCh38’) rg37.add_liftover(‘grch37_to_grch38.over.chain.gz’, rg38) gn = gn.annotate(new_locus=hl.liftover(gn.l…

How many partitions in the MT and the table? Generally, you can fix memory issues by increasing the number of partitions. I’d try doubling the number of partitions on both.

I have 67376 partitions for the MT and 10000 partitions for the table. Thanks for the suggestion. I will try to increase these numbers.

Hi, Hail Team! As you all know, I think Hail is fantastic and I am planning on using it for a dataset that is in hg19 that I’d like to liftover to hg38. One of my questions is: what is the difference between the Hail liftover function vs the one from Picard tools? Any thoughts?

Can I liftover a hail table from GRCH37 to GRCH38

Hail Query & hailctl

Topic		Replies	Views
Liftover from 38 to 37 Hail Query & hailctl	6	582	January 25, 2023
Liftover Range Exception and Support for chrom 'MT' Hail Query & hailctl	3	640	September 9, 2019
Error running Liftover of UK Biobank Hail Query & hailctl	7	1228	June 25, 2020
Potential liftover issue: Error summary: NoSuchElementException: key not found: GRCh37 Hail Query & hailctl	4	1368	December 6, 2021
Liftover NullPointerException Hail Query & hailctl	6	610	April 26, 2019

Can I liftover a hail table from GRCH37 to GRCH38

Related topics