gnomad_methods

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filter_vep_transcript_csqs does not work for passing list of CSQ terms

1

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...

mike-w-wilson

As suggested by Chris, we're filtering VDS to trios by `hl.vds.filter_samples`, which will greatly drop the number of variants to the ones with at least one ALT allele in the...

KoalaQin

klaricch

Also adds some functions to help transform the methylation data for annotation onto the context HT: - `transform_methylation_level` - `transform_grch37_methylation` - `transform_grch38_methylation` Tested with: ``` from gnomad.resources.grch38.gnomad import coverage, all_sites_an,...

jkgoodrich

jkgoodrich

I still need to add tests for the added function and modified function

jkgoodrich