bugfix: filter out null clinvar conditions. #1083
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bpblanken
commented
Apr 17, 2025
| lambda p: p.split(r':')[1], | ||
| ht.conditions, | ||
| # assumes the format 'MedGen#:condition;MedGen#:condition', e.g.'C0023264:Leigh syndrome' | ||
| conditions=hl.filter( |
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Note this changes the one-to-one alignment between submitters and conditions, but I don't think we're doing anything that pairing. It's already one-submitter-to-many-conditions in practice, we were just pulling the first one.
…seqr-loading-pipelines into benb/clinvar_missing_conditions
hanars
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Apr 17, 2025
bpblanken
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Apr 17, 2025
* feat: filter long alleles * trailing comma * Update validate_callset.py * bug: filter clinvar missing conditions (#1083)
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Noticed this while building schema for clinvar... this field requires Nulls, which we don't want.