I’m trying to get ensembl gene annotation text file to the genome version GRCh38.
I need human dataset of the Ensembl GRCh38 that work with hail.
I have BioMart version, but I keep getting errors like this:
Hail version: 0.2.49-11ae8408bad0
Error summary: HailException: Invalid interval ‘[Y:2784749-Y:2784853)’ found. Contig ‘Y’ is not in the reference genome ‘GRCh38’.
this is thr error I got after running this code:
gene_ht = gene_ht.transmute(interval = hl.locus_interval(gene_ht.chromosome,
I’m not from the US region, so the annotation db was not much of a help for me.
Thank you so much in advance!