kemalandClaude Opus 5.5
58e70bc894
- 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
89 lines
1.4 KiB
JSON
89 lines
1.4 KiB
JSON
{
|
|
"individuals": 30,
|
|
"regions": {
|
|
"GSTM1": {
|
|
"record": "HGSV_9691",
|
|
"concordant": 30,
|
|
"n": 30,
|
|
"rate": 1.0,
|
|
"truth_to_call_mismatches": {}
|
|
},
|
|
"UGT2B17": {
|
|
"record": "HGSV_63272",
|
|
"concordant": 30,
|
|
"n": 30,
|
|
"rate": 1.0,
|
|
"truth_to_call_mismatches": {}
|
|
},
|
|
"SULT1A1": {
|
|
"record": "HGSV_207805",
|
|
"concordant": 29,
|
|
"n": 30,
|
|
"rate": 0.9667,
|
|
"truth_to_call_mismatches": {
|
|
"2->1": 1
|
|
}
|
|
},
|
|
"CYP2A6.intron.7": {
|
|
"record": "HGSV_232737",
|
|
"concordant": 28,
|
|
"n": 30,
|
|
"rate": 0.9333,
|
|
"truth_to_call_mismatches": {
|
|
"3->2": 1,
|
|
"1->2": 1
|
|
}
|
|
},
|
|
"CYP2A6.exon.1": {
|
|
"record": "HGSV_232737",
|
|
"concordant": 29,
|
|
"n": 30,
|
|
"rate": 0.9667,
|
|
"truth_to_call_mismatches": {
|
|
"3->2": 1
|
|
}
|
|
},
|
|
"CYP2D6.exon.9": {
|
|
"record": "HGSV_247317",
|
|
"concordant": 25,
|
|
"n": 30,
|
|
"rate": 0.8333,
|
|
"truth_to_call_mismatches": {
|
|
"4->2": 1,
|
|
"3->2": 3,
|
|
"2->1": 1
|
|
}
|
|
},
|
|
"CYP2D6.intron.2": {
|
|
"record": "HGSV_247317",
|
|
"concordant": 25,
|
|
"n": 30,
|
|
"rate": 0.8333,
|
|
"truth_to_call_mismatches": {
|
|
"4->3": 1,
|
|
"3->2": 3,
|
|
"2->1": 1
|
|
}
|
|
},
|
|
"CYP2D6.p5": {
|
|
"record": "HGSV_247317",
|
|
"concordant": 28,
|
|
"n": 30,
|
|
"rate": 0.9333,
|
|
"truth_to_call_mismatches": {
|
|
"4->3": 1,
|
|
"2->1": 1
|
|
}
|
|
}
|
|
},
|
|
"overall": {
|
|
"concordant": 224,
|
|
"n": 240,
|
|
"rate": 0.9333
|
|
},
|
|
"gstt1_cn_distribution": {
|
|
"0": 5,
|
|
"1": 16,
|
|
"2": 9
|
|
}
|
|
} |