broadinstitute gnomad_methods issues

broadinstitute / gnomad_methods

Hail helper functions for the gnomAD project and Translational Genomics Group

https://gnomad.broadinstitute.org

MIT License

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issues

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Add `get_loftee_end_trunc_filter_expr` and `update_loftee_end_trunc_filter` to patch the LOFTEE END_TRUNC filter

#740 jkgoodrich opened 1 day ago
0
Change filter_mt_to_trios to also filter on vds

#739 KoalaQin closed 4 weeks ago
0
Add functions to check struct and array missingness

#738 klaricch opened 1 month ago
0
Add joint to public release

#737 KoalaQin closed 1 month ago
0
Add contig check to summarize_variants

#736 klaricch closed 1 month ago
0
gnomAD toolbox for gnomAD users

#735 KoalaQin closed 1 month ago
0
Add `get_mu_annotation_expr` function that prevents a shuffle from happening when annotating a HT with mutation rate and use in `annotate_with_mu`

#734 jkgoodrich opened 1 month ago
0
Add `assemble_constraint_context_ht` function to create a fully annotated context HT for computing constraint on

#733 jkgoodrich opened 1 month ago
0
Add `max_grpmax` option to `get_summary_stats_variant_filter_expr` for filtering by grpmax

#732 jkgoodrich closed 2 months ago
0
Add retain cdf option for median calculations when computing info fields

#731 klaricch closed 2 months ago
0
Update getting started guide with warning on versioning

#730 mike-w-wilson closed 2 months ago
0
Add `get_tissues_to_exclude` function to determine what tissues to exclude from transcript annotation calculations

#729 jkgoodrich closed 2 months ago
0
Unable to initialize google cluster according to guidelines

#728 wjwei-handsome closed 2 months ago
1
Fix `tx_filter_variants_by_csqs` to correctly handle the `ignore_splicing` parameter

#727 jkgoodrich closed 3 months ago
0
Update default vep version for context table resource

#726 ch-kr closed 3 months ago
0
Add `filter_meta_array` and change `filter_arrays_by_meta` to support more complex `items_to_filter` parameters by using `filter_meta_array`

#725 jkgoodrich opened 3 months ago
0
Add coverage_metric param to allow for different metrics of coverage and cov_model_type option to allow for linear or logarithmic

#724 klaricch closed 3 months ago
0
Meet with Talkowski Group Member / Others about LD Code

#723 matren395 closed 3 months ago
1
calculate constraint metrics per gen_anc

#722 klaricch closed 3 months ago
1
pext runtime changes

#721 jkgoodrich closed 3 months ago
0
Update setup.py for v0.8.1

#720 mike-w-wilson closed 4 months ago
0
Add vds list option to create vds

#719 mike-w-wilson closed 3 months ago
0
Add functions `fill_missing_key_combinations` and `missing_struct_expr`

#718 jkgoodrich closed 4 months ago
1
Dependabot assigns PRs automatically and only creates them for security updates

#717 mike-w-wilson closed 4 months ago
0
Add create_vds function that only supports creating from gvcfs

#716 mike-w-wilson closed 4 months ago
0
Bump the pip group in /docs with 2 updates

#715 dependabot[bot] opened 4 months ago
0
Deprecate `get_most_severe_consequence_for_summary` in favor of more flexible `get_most_severe_csq_from_multiple_csq_lists`

#714 jkgoodrich opened 5 months ago
0
Add `filter_vep_transcript_csqs_expr`, a version of `filter_vep_transcript_csqs` that takes and returns an ArrayExpression

#713 jkgoodrich closed 4 months ago
0
Bump urllib3 from 2.0.7 to 2.2.2 in /docs in the pip group across 1 directory

#712 dependabot[bot] opened 5 months ago
0
Update csq impact lists with v105 splice terms

#711 mike-w-wilson closed 5 months ago
4
Fix bug in `process_consequences` that was introduced when adding support for VEP without polyphen

#710 jkgoodrich closed 5 months ago
2
Fix `annotate_with_ht` to only use a semi-join when `filter_missing` is True

#709 jkgoodrich closed 5 months ago
0
Bump requests from 2.31.0 to 2.32.2 in /docs

#708 dependabot[bot] closed 5 months ago
0
filter_vep_transcript_csqs does not work for passing list of CSQ terms

#707 mike-w-wilson opened 6 months ago
1
Modify `filter_vep_transcript_csqs` to filter vep transcripts to MANE if exists otherwise canonical when both are TRUE

#706 jkgoodrich closed 6 months ago
0
Copy of Run code to calculate the average number of mutations per exome and genome in the v4 exome callset

#705 matren395 closed 6 months ago
0
Run code to calculate the average number of mutations per exome and genome in the v4 exome callset

#704 matren395 closed 6 months ago
0
Update VEP csqs in impact categories to match VEP

#703 mike-w-wilson closed 6 months ago
0
Bump requests from 2.31.0 to 2.32.0 in /docs

#702 dependabot[bot] closed 5 months ago
1
Add `get_summary_stats_variant_filter_expr` and `get_summary_stats_csq_filter_expr` to build filtering expressions for summary stats

#701 jkgoodrich closed 6 months ago
0
Bump jinja2 from 3.1.3 to 3.1.4 in /docs

#700 dependabot[bot] closed 5 months ago
0
Change the number of values for stat_union_gen_ancs to unknown

#699 KoalaQin closed 7 months ago
0
Add a space in joint filter info dict

#698 KoalaQin closed 7 months ago
0
Fix bug in joint filter dict

#697 mike-w-wilson closed 7 months ago
0
Add joint filters info dict

#696 KoalaQin closed 7 months ago
1
Add Stat Union to the info dict

#695 KoalaQin closed 7 months ago
0
Add explode_downsamplings function

#694 klaricch closed 7 months ago
0
Fix `generic_field_check` in validity_checks.py print of failed checks

#693 jkgoodrich closed 7 months ago
0
Bump idna from 3.4 to 3.7 in /docs

#692 dependabot[bot] closed 5 months ago
1
remove hardcoding of v4 in gnomad_gks

#691 klaricch closed 7 months ago
0