Mike Wilson
Mike Wilson
Add a module to the vep utils to remove 100% missing fields. This would cover https://github.com/broadinstitute/gnomad_qc/issues/186. There may be utility in generalizing the function to remove any field that is...
Currently, VersionedResources will throw a KeyError when a version of a resource is requested does not exist. We should handle this with a better error message, alerting the user that...
ClinVar releases a new VCF every month. gnomAD v3.1 used the same VCF/HT as v3 which dates to Sept 2019. The new ClinVar resource should be added to the reference...
Hail only allows `add_liftover` to be run once per reference genome. We'd like to add a liftover check using `has_liftover` and also standardize the chain files used during reference genome...
Add v4.1 to releases once release HTs are created and synced
Working on v4.0, we created the gnomad_methods function `split_vds_by_strata` which splits a vds based on a n expression. The desired behavior was to split a vds and maintain all alleles...
Mark and Konrad found that we have some variants labeled as intron when they should be splice region. The two example variants are https://gnomad.broadinstitute.org/variant/16-30959189-A-G?dataset=gnomad_r4 and https://gnomad.broadinstitute.org/variant/16-30959190-A-G?dataset=gnomad_r4. ![Screenshot 2024-05-08 at 10...
There is a bug here: https://github.com/broadinstitute/gnomad_methods/blob/019865838f993841a540e0b29d8d2f3b1333b1b8/gnomad/utils/vep.py#L788 The `most_severe_consequence` field is a top level `vep` field, at the same level as `transcript_consequences`, so the way this is currently built does not...