SimurgArray/scripts/pgx/demo36_identity.tsv at b96ae21c70aaf956756b2365cc60b4fca28b621c

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kemal c3e0681b6e 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

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1	# GSA v4 PGx demo (idats_Demo_36) sample identities: best match among the 3202 1000 Genomes 30x individuals
2	# by genotype concordance on 4647 chr22 SNPs with 1000G AF 0.05-0.95 (next best <= 0.91: relatives)
3	sample_id	individual	concordance	second_best	second_concordance
4	207895980019_R03C01	NA12875	0.9920	NA12865	0.7038
5	207895980019_R03C02	NA12156	0.9933	NA10831	0.7021
6	207895980019_R04C01	NA12156	0.9931	NA10831	0.7027
7	207895980019_R05C01	NA12044	0.9931	NA10857	0.6969
8	207895980019_R06C01	NA11992	0.9931	NA10860	0.6848
9	207895980019_R07C01	NA06993	0.9940	NA06991	0.7209
10	207895980019_R07C03	NA07019	0.9953	NA07056	0.7051
11	207895980019_R08C01	NA12239	0.9938	NA10847	0.7022
12	207895980019_R09C01	NA12716	0.9944	NA12707	0.6896
13	207895980019_R09C03	NA06991	0.9931	NA06993	0.7215
14	207895980019_R10C01	NA12878	0.9933	NA12892	0.7022
15	207895980019_R11C01	NA12760	0.9948	NA12752	0.7171
16	207895980019_R11C02	NA06985	0.9948	NA06991	0.6996
17	207895980019_R12C01	NA11993	0.9961	NA10860	0.7168
18	207895980019_R12C02	NA12003	0.9935	NA10838	0.6998
19	207895980019_R13C03	NA06994	0.9948	NA07029	0.7114
20	207895980019_R14C03	NA11993	0.9959	NA10860	0.7163
21	207895980019_R15C02	NA12003	0.9931	NA10838	0.6993
22	207895980035_R03C03	NA07029	0.9952	NA07000	0.7237
23	207895980035_R04C03	NA12892	0.9957	NA12878	0.7005
24	207895980035_R05C03	NA12248	0.9950	NA10835	0.7143
25	207895980035_R06C03	NA10846	0.9920	NA12145	0.7056
26	207895980035_R07C01	NA07000	0.9957	NA07029	0.7231
27	207895980035_R07C03	NA12155	0.9935	NA10831	0.6903
28	207895980035_R08C01	NA11832	0.9942	NA10855	0.7252
29	207895980035_R08C03	NA06993	0.9940	NA06991	0.7205
30	207895980035_R09C03	NA10838	0.9948	NA12004	0.7007
31	207895980035_R10C01	NA12813	0.9937	NA07045	0.9103
32	207895980035_R10C03	NA12249	0.9938	NA10835	0.6858
33	207895980035_R11C03	NA12812	0.9942	NA12801	0.7061
34	207895980035_R12C03	NA11881	0.9935	NA10859	0.7138
35	207895980035_R13C01	NA11995	0.9953	NA10861	0.6857
36	207895980035_R13C03	NA12248	0.9950	NA10835	0.7145
37	207895980035_R14C01	NA12891	0.9942	NA12878	0.6998
38	207895980035_R15C03	NA12043	0.9946	NA10857	0.7162
39	207895980042_R15C02	NA11832	0.9942	NA10855	0.7253

2.0 KiB Raw Blame History

2.0 KiB

Raw Blame History