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Add option to filter to releasable trios for generating trio stats #638
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@@ -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( | |||
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# 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
Back to you @klaricch! |
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lgtm
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