kemal 4d9efab2fc PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006) ...

fetch_sources.sh downloads PharmVar per-gene zips; pgx db build adds core alleles for genes CPIC does not
define (normalised against the FASTA, *1 = reference). Masks re-derived with the new variants. GeT-RM:
CYP3A4 15/15, CYP2A6 7/9; all comparable genes 154/168 (CYP1A2/CYP2C8 definitions differ from GeT-RM's).

2026-09-29 16:50:27 +01:00

..

build_cn_regions.py

PGx star alleles: pgx star-allele call (PGX-011..021), probe masks vs 1000G, GeT-RM validation (K-029)

2026-09-29 14:08:03 +01:00

demo36_identity.tsv

PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028)

2026-09-29 13:16:19 +01:00

derive_masks.py

derive_masks: keep pysam's downloaded tabix indexes in data/pgx/cache, not the working directory

2026-09-29 16:00:25 +01:00

fetch_sources.sh

PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006)

2026-09-29 16:50:27 +01:00

getrm_truth.py

PGx: all CPIC gene kinds — G6PD, variant-based, HLA tags, *0 CN genes (PGX-006/007/021)

2026-09-29 16:24:33 +01:00

validate_cn_truth.py

PGx star alleles: pgx star-allele call (PGX-011..021), probe masks vs 1000G, GeT-RM validation (K-029)

2026-09-29 14:08:03 +01:00

validate_star_getrm.py

PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006)

2026-09-29 16:50:27 +01:00