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Add option to filter to releasable trios for generating trio stats #638

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merged 4 commits into from
Oct 16, 2024

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KoalaQin
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@KoalaQin KoalaQin commented Sep 25, 2024

Update the run_generate_trio_stats function to filter the fam_ht to releasable trios (pat-mat-proband) only. It won't overwrite the existing output for all trios.

Tested:
5 trios from test VDS
5650d7690333482f856e50c4105864ff

3 releasable trios from test VDS
f70603af341244ae81f23d868d9945c3

@KoalaQin KoalaQin self-assigned this Sep 25, 2024
@KoalaQin KoalaQin changed the title Add options to filter to releasable trios only Add option to filter to releasable trios for generating trio stats Sep 25, 2024
@@ -666,6 +678,7 @@ def get_variant_qc_annotation_resources(
over_n_alleles: Optional[bool] = None,
combine_compute_info: bool = False,
true_positive_type: Optional[str] = None,
releasable_only: bool = False,
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for this function i would change the "releasable_only" param to "releasable_trios_only" to avoid potential confusion that the other steps are also being filtered to releasable here

@@ -462,6 +464,16 @@ def run_generate_trio_stats(

# Filter the variant data to bi-allelic sites.
vmt = vmt.filter_rows(hl.len(vmt.alleles) == 2)
if releasable_only:
meta = vmt.cols()
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could add a logger stating that filtering to releasable trios here

@KoalaQin KoalaQin removed the request for review from mike-w-wilson October 15, 2024 16:19
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KoalaQin commented Oct 16, 2024

Back to you @klaricch!
New test run: 579573c682b843118b4d99e659ba9250

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lgtm

@KoalaQin KoalaQin merged commit 70b1ff4 into main Oct 16, 2024
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@KoalaQin KoalaQin deleted the qh/trios_de_novo branch October 16, 2024 18:45
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3 participants