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If you could share any example files for the structural variant VCF 4.4 version with us, that would be amazing. That way, we could update our workflow as well.
Yes, please see COLO829v003T.purple.sv.vcf example file and ignore ##fileformat=VCFv4.2 in the header section.
GRIDSS uses HTSJDK which writes VCF version 4.2. So, yes, that technically makes it non-compliant with version 4.4. That said, the content of the actual records are compliant with the version 4.4 specification.
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