![]() So there are infelicities in all three - the specifications, gnomAD, and BCFtools - contributing to this problem. So it is also technically true that BCFtools is failing to process a valid VCF v4.2 file here. So gnomAD have produced valid VCF v4.2 files - but unfortunately the keys used are incompatible with VCF v4.3.Ä«CFtools (quite reasonably) takes advantage of the INFO/FORMAT key charset restrictions in its implementation (in particular, as we see here, in its query syntax) without implementing special cases for earlier VCF versions. VCF v4.2 has no restrictions on the characters in INFO/FORMAT keys, and does not mention the upcoming restrictions in later VCF versions. These gnomAD data files declare themselves as #fileformat=VCFv4.2, presumably because Picard/etc have only partial (reading only) support for VCF v4.3 (and prior to htsjdk 2.20.0 the Java tools had no support for v4.3). ![]() The situation is more complicated than that.
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