No error/warning for missing symbolic alternate allele description in header

EBIvariation / vcf-validator

Validation suite for Variant Call Format (VCF) files, implemented using C++11

Apache License 2.0

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No error/warning for missing symbolic alternate allele description in header #112

Closed eroller closed 6 years ago

eroller commented 6 years ago

I had a file with entries that had ALT column <DUP> but that ALT did not have a description in the vcf header. vcf-validator didn't generate an error or warning for this file. I looked in the vcf spec and didn't see this as a requirement, but perhaps vcf-validator should generate a warning for it?

eroller commented 6 years ago

My mistake. I did get a warning for this scenario:

Line 199: Alternate '<DUP>' is not listed in a valid meta-data ALT entry (warning)

jmmut commented 6 years ago

Yes, that is the expected behaviour. Glad you figured it out. Also, if this or any other part of the usage of the vcf-validator is unintuitive or hard to work with, please tell us.