diff --git a/gnomad_qc/v4/annotations/vrs_annotation_batch.py b/gnomad_qc/v4/annotations/vrs_annotation_batch.py index 610cab32a..f8114cc79 100644 --- a/gnomad_qc/v4/annotations/vrs_annotation_batch.py +++ b/gnomad_qc/v4/annotations/vrs_annotation_batch.py @@ -313,23 +313,10 @@ def main(args): batch_vrs.run() logger.info( - "Batch jobs executed, preparing to read in sharded VCF from prior step." - " Preparing list of files first using Hail's hadoop_ls method." + "Batch jobs executed, importing annotated shards into Hail Table..." ) - - annotated_file_dict = hl.utils.hadoop_ls( - f"gs://{working_bucket}/vrs-temp/annotated-shards/annotated.vcf/*" - ) - - annotated_file_list = [ - annotated_file_item["path"] for annotated_file_item in annotated_file_dict - ] - - logger.info("File list created. Now reading in annotated shards.") - - # Import all annotated shards ht_annotated = hl.import_vcf( - annotated_file_list, + f"gs://{working_bucket}/vrs-temp/annotated-shards/annotated.vcf/*", force_bgz=True, reference_genome=assembly, ).rows()