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Suggestions to per sample counts 4.1 PR #581

Merged
merged 19 commits into from
Mar 20, 2024
Merged

Suggestions to per sample counts 4.1 PR #581

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7f3423c
Add suggested edits to the per sample stats script
jkgoodrich Mar 15, 2024
bd486d7
get correct MT for genomes
jkgoodrich Mar 15, 2024
fd5a7bb
Merge branch 'main' of https://github.com/broadinstitute/gnomad_qc in…
jkgoodrich Mar 15, 2024
3469016
Fixes during testing
jkgoodrich Mar 15, 2024
1f48b90
Merge branch 'dm/per_sample_counts_4_1' of https://github.com/broadin…
jkgoodrich Mar 15, 2024
26451ce
check for struct expression
jkgoodrich Mar 15, 2024
84e5302
remove unneeded hl.struct
jkgoodrich Mar 15, 2024
f380f0f
add multiple aggregations to avoid a class too large error
jkgoodrich Mar 15, 2024
3b9c4f1
Apply suggestions from code review
jkgoodrich Mar 15, 2024
a05b4b1
Use _localize=False in the aggregation
jkgoodrich Mar 15, 2024
052262d
Merge branch 'jg/suggestions_to_per_sample_counts_4_1' of https://git…
jkgoodrich Mar 15, 2024
5c359c3
Checkpoint before print
jkgoodrich Mar 15, 2024
6d7e8ec
fix from testing
jkgoodrich Mar 15, 2024
46d1a01
Add filter to chr22 for release_ht
jkgoodrich Mar 18, 2024
d8247ed
Update gnomad_qc/v4/create_release/calculate_variant_statistics.py
jkgoodrich Mar 18, 2024
48862de
Add option to print stats
jkgoodrich Mar 18, 2024
949834f
Apply suggestions from code review
jkgoodrich Mar 19, 2024
f67be9e
Add option for rare variant AF cutoff
jkgoodrich Mar 19, 2024
a9a8cfd
Change arguments to skip so they don't all need to be included
jkgoodrich Mar 19, 2024
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