Issues with format from import_vcf for vcf.gz file

Hail Query & hailctl
1

Hi Hail developers,
I am a new hail user and was struggling to process my multi-sample vcf file with hail. I first tried to read in my file with the code below and create annotate another column:

import hail as hl
rt=hl.import_vcf(‘chr1_biallelic.vcf.gz’,force_bgz=True,reference_genome=“GRCh38”,drop_samples=True).rows()
rt = rt.annotate(variant=rt.CHROM + ‘:’ + rt.POSITION + “:” + rt.REF + “:” + rt.ALT)

However, running the third line gives me the following error:
AttributeError: Table instance has no field, method, or property 'CHROM’

Even though the CHROM header is present in my vcf.gz file, it’s not being noticed. Is it because of the metadata headers? Sorry if this is a basic question, I don’t have any other resources to rely on and couldn’t find any solutions online.

2

Take a look at the import_vcf docs starting with “Row fields” – Hail imports VCF files by converting the CHROM/POSITION fields to a single locus object mt.locus. You can access the chromosome and position with mt.locus.contig and mt.locus.position respectively.