kemal 7dc1fbc014 PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028) ...

- simurg/pgx/cn.py: per-region CN mixture, mu_c = delta + gamma*log2((c+1)/3), free lower CN-0 component,
  Hardy-Weinberg-constrained weights over haplotype copy numbers, EM from a grid of label starts.
- pipeline/pgx_cn.py: model file (.simurg-pgxcn), batch rules (PCN-004), per-sample CN VCF + tbi, batch and
  sample summaries.
- The GSA v4 PGx demo arrays are 30 CEPH/1000G individuals (scripts/pgx/demo36_identity.tsv); against NYGC 30x
  SV RD_CN 224/240 region calls agree (GSTM1, UGT2B17 30/30), in-sample (docs/validation/V2_pgx_cn.md).

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

..

P1_omni2141_summary.json

P1 validated on 1000 Genomes Omni2.5 (2141 vendor GTCs + IDATs)

2026-09-27 20:22:35 +01:00

P1.md

P1 validated on 1000 Genomes Omni2.5 (2141 vendor GTCs + IDATs)

2026-09-27 20:22:35 +01:00

P2_omni2141_summary.json

P2 validated on 2141 vendor GTCs (1000 Genomes Omni2.5)

2026-09-27 22:19:28 +01:00

P2.md

P2 validated on 2141 vendor GTCs (1000 Genomes Omni2.5)

2026-09-27 22:19:28 +01:00

P3_omni2141_summary.json

P3 validated: normalization bit-identical on 2141 vendor GTCs

2026-09-27 23:41:43 +01:00

P3.md

P3 validated: normalization bit-identical on 2141 vendor GTCs

2026-09-27 23:41:43 +01:00

P4_omni2141_summary.json

P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset

2026-09-28 01:21:49 +01:00

P4_preset_omni2141_summary.json

P5 validated on 2141 1000G samples; control-metric fixes (K-021)

2026-09-28 10:25:32 +01:00

P4.md

P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset

2026-09-28 01:21:49 +01:00

P5_omni2141_summary.json

P5 validated on 2141 1000G samples; control-metric fixes (K-021)

2026-09-28 10:25:32 +01:00

P5.md

P5 validated on 2141 1000G samples; control-metric fixes (K-021)

2026-09-28 10:25:32 +01:00

P6_gsa36_vs_gtc2vcf.json

P6 validated against GTCtoVCF too: zero unexplained genotype differences

2026-09-28 13:20:44 +01:00

P6_gsa36_vs_gtctovcf.json

P6 validated against GTCtoVCF too: zero unexplained genotype differences

2026-09-28 13:20:44 +01:00

P6.md

P6 complete: optional VCF fields, SNV+indel merging, auxiliary MNV loci, PLINK 2 .pgen

2026-09-28 14:29:42 +01:00

P7.md

P7: differential-testing harness (simurg compare) and nightly run on the Pi

2026-09-28 17:00:37 +01:00

P8_gse165845_summary.json

P8 complete: scientific validation on GSE165845 vs NYGC 30x and GIAB HG001

2026-09-28 19:47:34 +01:00

P8.md

P8 complete: scientific validation on GSE165845 vs NYGC 30x and GIAB HG001

2026-09-28 19:47:34 +01:00

P9_identity_360.json

P9 complete: compiled kernels validated (byte-identical, 78-80 GSA samples/min/core), scaling report

2026-09-28 22:32:48 +01:00

P9_scaling_gp3.json

P9 complete: compiled kernels validated (byte-identical, 78-80 GSA samples/min/core), scaling report

2026-09-28 22:32:48 +01:00

P9_scaling_ramdisk.json

P9 complete: compiled kernels validated (byte-identical, 78-80 GSA samples/min/core), scaling report

2026-09-28 22:32:48 +01:00

P9.md

P9 complete: compiled kernels validated (byte-identical, 78-80 GSA samples/min/core), scaling report

2026-09-28 22:32:48 +01:00

P10.md

P10 complete: packaging verified on fresh x86_64 and aarch64 VMs

2026-09-28 23:53:59 +01:00

V2_cn_gse165845_q10.json

v2 CN: real-data validation vs NYGC 30x SVs (interim), noise gate on normalised LRR (K-027)

2026-09-29 07:42:06 +01:00

V2_cn_gse165845_q20.json

v2 CN: real-data validation vs NYGC 30x SVs (interim), noise gate on normalised LRR (K-027)

2026-09-29 07:42:06 +01:00

V2_cn_synthetic_gsa36.json

v2 CN: synthetic implant evaluation (CYTO-022); reference GTC discovery follows symlinks

2026-09-29 01:30:07 +01:00

V2_cn.md

V2 CN: CYTO-042 results (precision up, mosaic calls halved); pi_run reports process memory without page cache

2026-09-29 12:20:40 +01:00

V2_methylation_vs_sesame.json

v2 methylation QC validated on minfiDataEPIC and against sesame (K-026)

2026-09-29 00:41:54 +01:00

V2_methylation.md

v2 methylation QC validated on minfiDataEPIC and against sesame (K-026)

2026-09-29 00:41:54 +01:00

V2_pgx_cn_demo36.json

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

V2_pgx_cn.md

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