-
Notifications
You must be signed in to change notification settings - Fork 256
Open
Labels
Description
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:
- Export a partitioned VCF with the necessary annotations. gnomAD has a method,
default_compute_infoto 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). - Execute VQSR in parallel using Hail Batch.
- Import the outputs of the VQSR jobs as a Hail Table.