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feat(report): flag a gene hit twice across engines, e.g. a deletion plus a variant on the other copy - #13
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geiresx wants to merge 6 commits into
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feat(report): flag a gene hit twice across engines, e.g. a deletion plus a variant on the other copy#13geiresx wants to merge 6 commits into
geiresx wants to merge 6 commits into
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…red before the rule Synthetic folders: a MUTYH exon deletion plus a heterozygous hit, the same with read-backed phase in trans and in cis, the 1q21.1 deletion plus the RBM8A low-expression allele, a 1/1 hit inside a deletion, SMN1 and HBA. Bead: pgp-pfw6.16
… variant on the other copy The carrier list joins the deletions of AnnotSV (class 4 and 5), step 35's interval table, its HBA count and Parascopy's SMN1 count with the ClinVar hits, gene by gene. Read-backed phase in trans, or a 1/1 hit inside the deletion (shown as hemizygous), gives biallelic; unknown phase gives possibly biallelic; cis gives no line. In the SF tier the deletion counts as one of the two variants MUTYH, BTD or ATP7B need. RBM8A's two TAR low-expression alleles join the carrier list's severity column. Bead: pgp-pfw6.16
Bead: pgp-pfw6.16
…e, never crash Bead: pgp-pfw6.16
…gene; AnnotSV deletions start after SV_start The RBM8A TAR alleles joined the severity column, which set them aside in the couple screen too: a TAR allele in one partner and an RBM8A deletion in the other no longer gave a child risk. A hypomorph now counts when the other partner has a full loss of function in the same gene; two hypomorphs, or one alone, stay set aside. AnnotSV's SV_start is the base before the deleted bases, so a 1/1 call there is no longer relabelled hemizygous.
… HIGH-impact phase The SF two-hit note is now attached only to the variant that pairs with the deletion, read-backed cis wins over the inside-deletion rule, HIGH-impact records keep their phase set, a gene AnnotSV names that ends at the padding base gets no pair, 0 alpha-globin genes pair with nothing, and an unreadable carrier list is a note on the SF card.
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GeiserX#281