gnomad_methods

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Prepare code for sites HT release

1

jkgoodrich

Add generic constraint functions

1

Add generic functions that were in `gnomad_lof` repo.

averywpx

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...

mike-w-wilson

Initial upload of VQSR workflow

11

Hi @jkgoodrich , @konradjk, cc @wlu04. Please have a look at the VQSR workflow and review. I decided to put resources file paths and parameters required for the workflow to...

LindoNkambule

### What you did: We want to use the ancestry classification tool to predict genetic ancestry of UKBB samples. (https://gnomad.broadinstitute.org/news/2021-09-using-the-gnomad-ancestry-principal-components-analysis-loadings-and-random-forest-classifier-on-your-dataset/) ### What happened: There is an error of "TypeError: object...

Jingning-Zhang

Block gzipped GENCODE files

1

The GENCODE GTF files associated with gnomAD annotations are occasionally useful. For example, they are needed to get the gene and transcript version numbers for VEP annotations for Ensembl transcripts....

nawatts

jkgoodrich

Fix ref_allele_mismatch in liftover_expr for indel variants

2

Hi, it seems the current `ref_allele_mismatch` doesn't work when the original reference allele has more than one bp. This PR fixes the issue. Additionally, I found there are `ref_allele_mismatch` cases...

mkanai

Update test_resource_utils.py to eliminate the requester-pays resource testing

1

I'm planning to archive the gs://gnomad-public-requester-pays data, so it probably doesn't make sense to maintain functions that call data from that bucket: https://github.com/broadinstitute/gnomad_methods/blob/e625c03b4f5e4d60b1b7c15402eeeab7a92ea3ea/tests/resources/test_resource_utils.py

gtiao

gtiao