Here is the view of one VCF file I have:
I am joining 10 such VCFs using VariantDatasetCombiner, and got the following error message:
AttributeError Traceback (most recent call last)
Cell In[19], line 18
15 gvcfs = [‘file:///’ + os.path.abspath(vcf) for vcf in vcf_files]
17 # Create the VariantDatasetCombiner
—> 18 combiner = hl.vds.new_combiner(
19 output_path=output_path,
20 temp_path=temp_path,
21 gvcf_paths=gvcfs,
22 use_exome_default_intervals=True
23 )
25 # Run the combiner
26 combiner.run()
File ~/anaconda3/envs/ds/lib/python3.10/site-packages/hail/vds/combiner/variant_dataset_combiner.py:637, in new_combiner(failed resolving arguments)
635 gvcf_type = mt._type
636 if gvcf_reference_entry_fields_to_keep is None:
→ 637 rmt = mt.filter_rows(hl.is_defined(mt.info.END))
638 gvcf_reference_entry_fields_to_keep = defined_entry_fields(rmt, 100_000) - {‘GT’, ‘PGT’, ‘PL’}
639 if vds is None:
File ~/anaconda3/envs/ds/lib/python3.10/site-packages/hail/expr/expressions/typed_expressions.py:1776, in StructExpression.getattr(self, item)
1774 return self.dict[item]
1775 else:
→ 1776 raise AttributeError(get_nice_attr_error(self, item))
AttributeError: StructExpression instance has no field, method, or property ‘END’
Hint: use ‘describe()’ to show the names of all data fields.
How should I fix it? Thanks!