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Script to compute combined FAF of v4 genomes and exomes #403

Merged
merged 40 commits into from
Oct 16, 2023
Merged

Script to compute combined FAF of v4 genomes and exomes #403

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9adcf5e
Copy of v3 compare freqs to v4
jkgoodrich Aug 22, 2023
b961693
Modify compare freqs for v4
jkgoodrich Aug 23, 2023
08804ef
clean up cochran_mantel_haenszel_test
jkgoodrich Aug 23, 2023
b172649
Add resources and docstrings
jkgoodrich Aug 24, 2023
cc2c665
Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in…
jkgoodrich Sep 14, 2023
51848ae
change input to freq_ht & test on one gene
KoalaQin Sep 22, 2023
9ff063a
removed combined_faf temporarily
KoalaQin Sep 22, 2023
4fd6064
minor editing for pops
KoalaQin Sep 22, 2023
a16ec9b
Merge remote-tracking branch 'origin' into qh/combined_faf
KoalaQin Sep 22, 2023
62ff299
change to use genomes release_sites
KoalaQin Sep 22, 2023
10881a0
Merge remote-tracking branch 'origin' into qh/combined_faf
KoalaQin Sep 22, 2023
c846c20
calcultate faf/grpmax if unavailable in freq_ht & rename popmax to gr…
KoalaQin Sep 24, 2023
af05bfe
add statsmodels in requirements-dev.txt
KoalaQin Sep 25, 2023
8cae8ca
reformat with black
KoalaQin Sep 25, 2023
190d517
remove potential idx duplicates
KoalaQin Sep 25, 2023
52ae80f
Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in…
jkgoodrich Sep 25, 2023
9b3573d
Merge branch 'jg/combined_faf' of https://github.com/broadinstitute/g…
jkgoodrich Sep 25, 2023
3b60904
add function to calculate fafmax/pop for faf95 and faf99
KoalaQin Sep 25, 2023
8a737cc
fafmax must be greater than 0
KoalaQin Sep 25, 2023
19815ed
address review comments
KoalaQin Sep 28, 2023
e2533bd
add TODO for passing variant_qc HT for filtering
KoalaQin Sep 28, 2023
813c5b3
annotate joint_fafmax directly from fax_expr output
KoalaQin Sep 28, 2023
0050c1c
change name of faf_max function
KoalaQin Oct 5, 2023
01d35a7
Merge pull request #446 from broadinstitute/qh/combined_faf
jkgoodrich Oct 9, 2023
8892dc3
Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in…
jkgoodrich Oct 12, 2023
ad5f413
Get PCSK9 test working with test genomes HT
jkgoodrich Oct 13, 2023
4458498
Change to work with exome and genome frequency data
jkgoodrich Oct 13, 2023
33a82fa
Address review comments
jkgoodrich Oct 13, 2023
44ac53e
Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in…
jkgoodrich Oct 13, 2023
894028f
Temp change for testing
jkgoodrich Oct 13, 2023
ca0e9a2
fix use of filter_arrays_by_meta
jkgoodrich Oct 13, 2023
27f8a20
Add checkpoint to avoid error
jkgoodrich Oct 13, 2023
15e93ba
apply_keep_to_only_items_in_filter -> exact_match
jkgoodrich Oct 13, 2023
9f805f4
Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in…
jkgoodrich Oct 13, 2023
b176054
Add versions to global annotation and finalize
jkgoodrich Oct 15, 2023
8045e37
Merge pull request #486 from broadinstitute/jg/combined_faf_final
jkgoodrich Oct 16, 2023
2fadc4a
Apply suggestions from code review
jkgoodrich Oct 16, 2023
775a42c
Add review suggestions
jkgoodrich Oct 16, 2023
187041e
Update gnomad_qc/v4/create_release/create_combined_faf_release_ht.py
jkgoodrich Oct 16, 2023
90aeff0
faf_meta to literal
jkgoodrich Oct 16, 2023
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