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Merged
merged 34 commits into from
Oct 19, 2023
Merged

Validity check v4 exomes #487

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4b09860
Initial commit w imports
mike-w-wilson Oct 12, 2023
e26f73c
Pipeline resources
mike-w-wilson Oct 13, 2023
d429050
Add validated release resource
mike-w-wilson Oct 13, 2023
761aec6
Add test filter and rough layout
mike-w-wilson Oct 13, 2023
d1f8fc6
Unfurl freq,faf,grpmax,age_hists
mike-w-wilson Oct 13, 2023
57cd0e8
Updates to creation of unfurled data
mike-w-wilson Oct 13, 2023
4cb3ff0
Add age_hists to unfurled data
mike-w-wilson Oct 14, 2023
78ff9c5
Update sites,vqsr,as fields, and add joint fields
mike-w-wilson Oct 14, 2023
339dd80
Update field removal
mike-w-wilson Oct 14, 2023
4190db0
Add arg parse and vcf_info_dict
mike-w-wilson Oct 14, 2023
6b3061b
Process VEP_CSQ_HEADER to drop polyphen and sift
mike-w-wilson Oct 14, 2023
ce6dffb
Pass args for validate_t
mike-w-wilson Oct 15, 2023
ba9a80c
Fix resource collection
mike-w-wilson Oct 15, 2023
b69c46c
Add verbose to args and add test HT, comment out real code
mike-w-wilson Oct 15, 2023
9d9baec
Fix joint FAF check from adding reg grpmax again
mike-w-wilson Oct 16, 2023
276fb76
More joint fixes
mike-w-wilson Oct 16, 2023
1299f0e
Merge branch 'main' into mw/validity_check_v4_exomes
mike-w-wilson Oct 17, 2023
dd900b8
Whoops, we want the subset sum check
mike-w-wilson Oct 17, 2023
13e8243
Add joint fafmax to info
mike-w-wilson Oct 18, 2023
502d011
update test file
mike-w-wilson Oct 18, 2023
37d987c
Get around clas too large error during missingness checks
mike-w-wilson Oct 18, 2023
859e1b1
Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in…
jkgoodrich Oct 18, 2023
1f80c70
Add only_het to info checks
mike-w-wilson Oct 18, 2023
b8e3e13
Add pprint globals and global and row length check
mike-w-wilson Oct 18, 2023
d1cd4a0
Update len compare call
mike-w-wilson Oct 19, 2023
73fdbc7
Update monoallelic to site_gt_check
mike-w-wilson Oct 19, 2023
aebdc90
Update to new variable name in validity checks
mike-w-wilson Oct 19, 2023
76e4add
Update to new variable name in validity checks
mike-w-wilson Oct 19, 2023
4028843
Add check for retired terms in globals
mike-w-wilson Oct 19, 2023
2bf710f
Add sib singletons and update calls to validate_release_t
mike-w-wilson Oct 19, 2023
b93c6c4
Update site_gt_check_expr to dict for monoallelic
mike-w-wilson Oct 19, 2023
0913c5b
Remove testing ht
mike-w-wilson Oct 19, 2023
18edaa1
File rename
mike-w-wilson Oct 19, 2023
3ef1360
Apply suggestions from code review
mike-w-wilson Oct 19, 2023
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2 changes: 1 addition & 1 deletion gnomad_qc/v3/create_release/prepare_vcf_data_release.py
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Original file line number Diff line number Diff line change
Expand Up @@ -931,7 +931,7 @@ def main(args): # noqa: D103
sample_sum_sets_and_pops=parameter_dict["sample_sum_sets_and_pops"],
missingness_threshold=0.5,
variant_filter_field="AS_VQSR",
monoallelic_expr=prepared_vcf_ht.info.monoallelic,
site_gt_check_expr={"monoallelic": prepared_vcf_ht.info.monoallelic},
verbose=args.verbose,
single_filter_count=True,
)
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