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ffaa3c5cdd
progress for 141/84: annotate 10/84, oncokb 1/84 every 10, GTF indexed
main
Matiq
2026-09-09 00:29:03 +03:00
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baa87ea048
fix OncoKB endpoint byHgvsVariant->byGenomicChange (GRCh38)
Matiq
2026-09-08 23:31:01 +03:00
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1f28f60bc0
fix ClinVar header #AlleleID + GRCh38 filter (was UnboundLocalError)
Matiq
2026-09-08 23:07:30 +03:00
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c20f61240f
ClinVar P/L + VAF>20% default for online
Matiq
2026-09-07 01:24:11 +03:00
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fb99880b80
README: threads, VCF filtering, annotation (GENCODE/OncoKB), VAF filter
Matiq
2026-09-07 01:05:49 +03:00
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8f8d728edd
pick best transcript per variant (1:1) default, --all-transcripts for expansion
Matiq
2026-09-07 01:00:58 +03:00
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9f4312ba3a
offline all-transcripts via GENCODE GTF + VAF>10% filter
Matiq
2026-09-07 00:47:51 +03:00
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b33f8c28a2
fix hang: offline mode, short timeouts, progress for large clean sets
Matiq
2026-09-07 00:34:25 +03:00
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ea8f531211
all transcripts via Ensembl REST (expand per variant, pan-cancer)
Matiq
2026-09-06 20:20:48 +03:00
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a3589279b9
annotate clean variants: Gen/HGVS/Effect + ACMG + AMP/Onco pan-cancer -> Excel
Matiq
2026-09-06 19:19:19 +03:00
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4e19fbdb8a
replace TSV with CSV for variant outputs
Matiq
2026-09-06 18:47:00 +03:00
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0f40945d58
parallel: auto threads (n-1, capped at 8)
Matiq
2026-09-06 18:27:54 +03:00
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5385f76447
filter damaged variants: clean output + VCF filtering
Matiq
2026-09-06 18:18:29 +03:00
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5fe6298926
README: methodology, usage, outputs, classification, validation
Matiq
2026-08-14 20:27:31 +03:00
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360479653a
FFPE deamination QC pipeline
Matiq
2026-08-14 20:25:49 +03:00
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eaa0bad7a8
Initial commit
Matiq
2026-08-14 20:25:38 +03:00