populationgenomics / talos

Rare Disease variant reanalysis tool

MIT License

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Mt to vcf updates #430

Closed MattWellie closed 2 months ago

MattWellie commented 2 months ago

Fixes

The VCF-to-MT process wasn't quite there
Neither was the example workflow script

Proposed Changes

Example script creates the output folder prior to starting, and provides all arguments required to CreateTalosHTML
Entrypoint correction for vcf_to_mt's console command
A few not-required fields removed from the Hail structure audit

VCF-to-MT

Some fields are renamed... the differences in output between VEP's JSON and VCF annotation are frustrating and many
AC/AF/AN/variant_class/geneIds are all slotted into the correct part of the schema