Change filter_mt_to_trios to also filter on vds #739
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klaricch
requested changes
Oct 30, 2024
KoalaQin
changed the title
klaricch
requested changes
Oct 31, 2024
gnomad/sample_qc/relatedness.py
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| if isinstance(t, hl.MatrixTable): | ||
| t = t.filter_cols(hl.is_defined(fam_ht[t.col_key])) | ||
| elif isinstance(t, hl.vds.VariantDataset): | ||
| t = hl.vds.filter_samples(t, fam_ht) |
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will the loss of sites impact the trio stats?
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You mean for the ones that are present in these trios?
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I checked this variant, (chr1:12648 ["T","G"]), which has a de novo raw in 1 child, in the trio_stats from last year and the new one, an for parents and children as in raw and adj certainly changed using filter_samples, but it was called as de novo raw either way.
klaricch
requested changes
Oct 31, 2024
klaricch
approved these changes
Nov 1, 2024
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As suggested by Chris, we're filtering VDS to trios by
hl.vds.filter_samples, which will greatly drop the number of variants to the ones with at least one ALT allele in the trio samples; Also, this function has been only used once in gnomad_qc,annotate_adjhas been used twice before, it will be removed from this function.It will not pass the checks if I changed the function name, should I just write another function?