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Description
VCF version 4.5 contains the changes we developed as part of our work developing the Scalable Variant Call Representation.
As the developers and drivers of these changes, we should fully support v4.5 via import to VDS and export from VDS.
Current checklist. May be extended over time:
- Prefer
LENoverENDfor reference blocks. (Begins in [query/vds] Add LEN field to VDS #14675) - Update the combiner to convert to
LENfrom INFOEND(Part of [query/vds] Add LEN field to VDS #14675). - Update
to_dense_mtto useLEN(we think it may be more efficient). - Add VDS to VCF export. ([query] Teach hail to export a VDS to an SVCR-VCF #14743)
- Add Sparse VCF to VDS import. ([query] Teach hail to export a VDS to an SVCR-VCF #14743)
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'Official' non-ref genotype(not part of this issue)<*>support? - Make sure that we output well formed VCF 4.5, this includes things like VCF 4.4's phased haploid calls (this will also require updates to our parser)
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