Matiq/ffpe_damage
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fb99880b80fc416392bcb760d85d7e28c09614d1
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5 Commits
Author SHA1 Message Date
Matiq 8f8d728edd pick best transcript per variant (1:1) default, --all-transcripts for expansion 
- offline GTF now picks MANE>appris1>canonical>basic>protein_coding (318 vs 3018 rows at VAF>10%)
- online Ensembl REST likewise picks best (mane_select/canonical)
- --all-transcripts restores previous all-transcripts behavior
 2026-09-07 01:00:58 +03:00
Matiq 9f4312ba3a offline all-transcripts via GENCODE GTF + VAF>10% filter 
- GENCODE v44 50M (252k transcripts) for offline gene expansion (1 variant -> N rows)
- --min-vaf/--min-depth filter before annotation (3501 -> 318 at VAF>10%)
- --gtf support, --offline now uses GTF (no network, no VEP cache needed)
- pan-cancer OncoKB retained for online mode
 2026-09-07 00:47:51 +03:00
Matiq b33f8c28a2 fix hang: offline mode, short timeouts, progress for large clean sets 2026-09-07 00:34:25 +03:00
Matiq ea8f531211 all transcripts via Ensembl REST (expand per variant, pan-cancer) 
- vep_annotate now iterates all transcript_consequences
- timeout 15s, graceful fallback to single placeholder row
 2026-09-06 20:20:48 +03:00
Matiq a3589279b9 annotate clean variants: Gen/HGVS/Effect + ACMG + AMP/Onco pan-cancer -> Excel 
- all transcripts mode (VEP no_pick fallback to best transcript via Ensembl REST)
- HGVS c.6713C>T p.(Pro2238Leu) style, Type/Effect, VAF, PAF(empty), ACMG ClinVar+InterVar (VUS placeholder), AMP/Onco via OncoKB (token ~/.config/oncokb/token, tumor_type All Solid Tumors)
- Excel .xlsx styled (color by ACMG/AMP, filters, frozen header)
 2026-09-06 19:19:19 +03:00