add hail sample_qc metrics #1046
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bpblanken
reviewed
Feb 25, 2025
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| def run_hail_sample_qc(mt: hl.MatrixTable, sample_type: SampleType) -> hl.MatrixTable: | ||
| mt = filter_to_autosomes(mt) | ||
| mt = hl.split_multi_hts(mt) |
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can this use the split_multi_hts wrapper?
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this comes from the old script, but I'm thinking it might not be necessary since the mt is our validated callset on which we already call split_multi_hts
matren395
reviewed
Feb 26, 2025
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| HAIL_QC_METRICS = [ | ||
| 'n_snp', | ||
| 'r_ti_tv', | ||
| 'r_insertion_deletion', | ||
| 'n_insertion', | ||
| 'n_deletion', | ||
| 'r_het_hom_var', | ||
| ] |
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only brief note: we know that all of these are used and relevant, right ?
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| strat_ht = mt.cols() | ||
| qc_metrics = {metric: strat_ht.sample_qc[metric] for metric in sample_qc_metrics} | ||
| strata = {'qc_pop': strat_ht.qc_pop} |
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Suggested change
| strata = {'qc_pop': strat_ht.qc_pop} | |
| strata = {'gq_gen_anc': strat_ht. gq_gen_anc} |
this is already annotated by then, yea ?
| return annotate_qc_gen_anc(mt) | ||
| mt = annotate_qc_gen_anc(mt) | ||
| mt = run_hail_sample_qc(mt, sample_type) | ||
| return mt.drop('qc_pop') |
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you could probably do this sooner, unless u really want to run sample_qc while stratifying on only the default (90%) genetic ancestry inference
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adds hail's
sample_qcmetrics to sample_qc json