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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

merged 40 commits into from
Oct 16, 2023

Commits on Aug 22, 2023

  1. Copy of v3 compare freqs to v4

    @jkgoodrich
    jkgoodrich committed Aug 22, 2023
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Commits on Aug 23, 2023

  1. Modify compare freqs for v4

    @jkgoodrich
    jkgoodrich committed Aug 23, 2023
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  2. clean up cochran_mantel_haenszel_test

    @jkgoodrich
    jkgoodrich committed Aug 23, 2023
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Commits on Aug 24, 2023

  1. Add resources and docstrings

    @jkgoodrich
    jkgoodrich committed Aug 24, 2023
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Commits on Sep 14, 2023

  1. Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in… 

    …to jg/combined_faf

# Conflicts:
#	gnomad_qc/v4/resources/annotations.py
    @jkgoodrich
    jkgoodrich committed Sep 14, 2023
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Commits on Sep 22, 2023

  1. change input to freq_ht & test on one gene

    @KoalaQin
    KoalaQin committed Sep 22, 2023
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  2. removed combined_faf temporarily

    @KoalaQin
    KoalaQin committed Sep 22, 2023
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  3. minor editing for pops

    @KoalaQin
    KoalaQin committed Sep 22, 2023
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  4. Merge remote-tracking branch 'origin' into qh/combined_faf

    @KoalaQin
    KoalaQin committed Sep 22, 2023
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  5. change to use genomes release_sites

    @KoalaQin
    KoalaQin committed Sep 22, 2023
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  6. Merge remote-tracking branch 'origin' into qh/combined_faf

    @KoalaQin
    KoalaQin committed Sep 22, 2023
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Commits on Sep 24, 2023

  1. calcultate faf/grpmax if unavailable in freq_ht & rename popmax to gr… 

    …pmax
    @KoalaQin
    KoalaQin committed Sep 24, 2023
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Commits on Sep 25, 2023

  1. add statsmodels in requirements-dev.txt

    @KoalaQin
    KoalaQin committed Sep 25, 2023
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  2. reformat with black

    @KoalaQin
    KoalaQin committed Sep 25, 2023
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  3. remove potential idx duplicates

    @KoalaQin
    KoalaQin committed Sep 25, 2023
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  4. Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in… 

    …to jg/combined_faf
    @jkgoodrich
    jkgoodrich committed Sep 25, 2023
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  5. Merge branch 'jg/combined_faf' of https://github.com/broadinstitute/g… 

    …nomad_qc into qh/combined_faf
    @jkgoodrich
    jkgoodrich committed Sep 25, 2023
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  6. add function to calculate fafmax/pop for faf95 and faf99

    @KoalaQin
    KoalaQin committed Sep 25, 2023
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  7. fafmax must be greater than 0

    @KoalaQin
    KoalaQin committed Sep 25, 2023
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Commits on Sep 28, 2023

  1. address review comments

    @KoalaQin
    KoalaQin committed Sep 28, 2023
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  2. add TODO for passing variant_qc HT for filtering

    @KoalaQin
    KoalaQin committed Sep 28, 2023
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  3. annotate joint_fafmax directly from fax_expr output

    @KoalaQin
    KoalaQin committed Sep 28, 2023
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Commits on Oct 5, 2023

  1. change name of faf_max function

    @KoalaQin
    KoalaQin committed Oct 5, 2023
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Commits on Oct 9, 2023

  1. Merge pull request #446 from broadinstitute/qh/combined_faf 

    Script to compute combined FAF of v4 genomes and exomes
    @jkgoodrich
    jkgoodrich authored Oct 9, 2023
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Commits on Oct 12, 2023

  1. Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in… 

    …to jg/combined_faf
    @jkgoodrich
    jkgoodrich committed Oct 12, 2023
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Commits on Oct 13, 2023

  1. Get PCSK9 test working with test genomes HT

    @jkgoodrich
    jkgoodrich committed Oct 13, 2023
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  2. Change to work with exome and genome frequency data

    @jkgoodrich
    jkgoodrich committed Oct 13, 2023
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  3. Address review comments

    @jkgoodrich
    jkgoodrich committed Oct 13, 2023
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  4. Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in… 

    …to jg/combined_faf
    @jkgoodrich
    jkgoodrich committed Oct 13, 2023
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  5. Temp change for testing

    @jkgoodrich
    jkgoodrich committed Oct 13, 2023
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  6. fix use of filter_arrays_by_meta

    @jkgoodrich
    jkgoodrich committed Oct 13, 2023
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  7. Add checkpoint to avoid error

    @jkgoodrich
    jkgoodrich committed Oct 13, 2023
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  8. apply_keep_to_only_items_in_filter -> exact_match

    @jkgoodrich
    jkgoodrich committed Oct 13, 2023
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  9. Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in… 

    …to jg/combined_faf

# Conflicts:
#	gnomad_qc/v4/resources/annotations.py
    @jkgoodrich
    jkgoodrich committed Oct 13, 2023
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Commits on Oct 15, 2023

  1. Add versions to global annotation and finalize

    @jkgoodrich
    jkgoodrich committed Oct 15, 2023
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Commits on Oct 16, 2023

  1. Merge pull request #486 from broadinstitute/jg/combined_faf_final 

    Add code for creating the final combined FAF release HT
    @jkgoodrich
    jkgoodrich authored Oct 16, 2023
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  2. Apply suggestions from code review 

    Co-authored-by: Mike Wilson <[email protected]>
    @jkgoodrich @mike-w-wilson
    jkgoodrich and mike-w-wilson authored Oct 16, 2023
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  3. Add review suggestions

    @jkgoodrich
    jkgoodrich committed Oct 16, 2023
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  4. Update gnomad_qc/v4/create_release/create_combined_faf_release_ht.py 

    Co-authored-by: Mike Wilson <[email protected]>
    @jkgoodrich @mike-w-wilson
    jkgoodrich and mike-w-wilson authored Oct 16, 2023
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  5. faf_meta to literal

    @jkgoodrich
    jkgoodrich committed Oct 16, 2023
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