 Matiq
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9f4312ba3a
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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
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2026-09-07 00:47:51 +03:00 |
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Matiq
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a3589279b9
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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)
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2026-09-06 19:19:19 +03:00 |
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