vcf: Failed filter names should disallow "PASS" and MISSING

Open zaeleus opened this issue 2 years ago • 1 comments

This in regard to The Variant Call Format Specification: VCFv4.4 and BCFv2.2 (2023-01-27).

§ 1.6.1.7 "FILTER" specializes "PASS", a case if the position passes all filters. Otherwise, a list of filter names that failed is used. The current description disallows "0" but does not mention whether "PASS" or "." (MISSING) are valid as failed filter names, e.g., "q10;PASS" or "q10;.". If these are not allowed, it should be made explicit.

Apr 13 '23 20:04 zaeleus

There also exists a related failed test case that disallows MISSING in a list of filters: test/vcf/4.3/failed/failed_body_filter_000.vcf.

May 01 '23 21:05 zaeleus