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Implement support for VQSR in QoB #12905

@danking

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@danking

After using the VDS combiner to produce a joint-called dataset, a user needs to run Allele-Specific Variant Quality Score Recalibration. DSP maintains some documentation on AS-VQSR as well as the original VQSR.

AS-VQSR is an arbitrary program which we do not want to link into our codebase. We will only be support VQSR in QoB. The method requires three steps:

  1. Export a partitioned VCF with the necessary annotations. gnomAD has a method, default_compute_info to produce these annotations from a sparse MT. We need to update that to support VDS (and, I suppose, its best to also support dense matrix tables).
  2. Execute VQSR in parallel using Hail Batch.
  3. Import the outputs of the VQSR jobs as a Hail Table.

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