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

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
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kemalandClaude Opus 5.5 committed 2026-09-29 13:16:19 +01:00
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scripts/pgx/demo36_identity.tsv
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# GSA v4 PGx demo (idats_Demo_36) sample identities: best match among the 3202 1000 Genomes 30x individuals
# by genotype concordance on 4647 chr22 SNPs with 1000G AF 0.05-0.95 (next best <= 0.91: relatives)
sample_id individual concordance second_best second_concordance
207895980019_R03C01 NA12875 0.9920 NA12865 0.7038
207895980019_R03C02 NA12156 0.9933 NA10831 0.7021
207895980019_R04C01 NA12156 0.9931 NA10831 0.7027
207895980019_R05C01 NA12044 0.9931 NA10857 0.6969
207895980019_R06C01 NA11992 0.9931 NA10860 0.6848
207895980019_R07C01 NA06993 0.9940 NA06991 0.7209
207895980019_R07C03 NA07019 0.9953 NA07056 0.7051
207895980019_R08C01 NA12239 0.9938 NA10847 0.7022
207895980019_R09C01 NA12716 0.9944 NA12707 0.6896
207895980019_R09C03 NA06991 0.9931 NA06993 0.7215
207895980019_R10C01 NA12878 0.9933 NA12892 0.7022
207895980019_R11C01 NA12760 0.9948 NA12752 0.7171
207895980019_R11C02 NA06985 0.9948 NA06991 0.6996
207895980019_R12C01 NA11993 0.9961 NA10860 0.7168
207895980019_R12C02 NA12003 0.9935 NA10838 0.6998
207895980019_R13C03 NA06994 0.9948 NA07029 0.7114
207895980019_R14C03 NA11993 0.9959 NA10860 0.7163
207895980019_R15C02 NA12003 0.9931 NA10838 0.6993
207895980035_R03C03 NA07029 0.9952 NA07000 0.7237
207895980035_R04C03 NA12892 0.9957 NA12878 0.7005
207895980035_R05C03 NA12248 0.9950 NA10835 0.7143
207895980035_R06C03 NA10846 0.9920 NA12145 0.7056
207895980035_R07C01 NA07000 0.9957 NA07029 0.7231
207895980035_R07C03 NA12155 0.9935 NA10831 0.6903
207895980035_R08C01 NA11832 0.9942 NA10855 0.7252
207895980035_R08C03 NA06993 0.9940 NA06991 0.7205
207895980035_R09C03 NA10838 0.9948 NA12004 0.7007
207895980035_R10C01 NA12813 0.9937 NA07045 0.9103
207895980035_R10C03 NA12249 0.9938 NA10835 0.6858
207895980035_R11C03 NA12812 0.9942 NA12801 0.7061
207895980035_R12C03 NA11881 0.9935 NA10859 0.7138
207895980035_R13C01 NA11995 0.9953 NA10861 0.6857
207895980035_R13C03 NA12248 0.9950 NA10835 0.7145
207895980035_R14C01 NA12891 0.9942 NA12878 0.6998
207895980035_R15C03 NA12043 0.9946 NA10857 0.7162
207895980042_R15C02 NA11832 0.9942 NA10855 0.7253
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