ArrayTrain: BIC-selected unbounded θ mixtures + HWE-guided labelling
Fixed θ windows mislabelled compressed/asymmetric loci (2-cluster loci: 1418 vs 186 errors). Now 1/2/3-component mixtures chosen by BIC, labelled by HWE goodness of fit plus weak position and gap priors, split clusters merged. GSE165845 chr22 vs 1000G 30x (240 arrays): concordance 99.44 % (v1 99.27 %, vendor EGT 99.46 %), NRD 1.30 % (1.89 %, 1.23 %), call rate 99.61 %. docs/validation/V2_arraytrain.md, K-030; plan §12, CLI-038.
This commit is contained in:
1 parent
adad0efb08
commit
1eb7ea8154
6 files changed
+304
-58
No files matched your search
@@ -0,0 +1,28 @@
|
||||
{
|
||||
"dataset": "GSE165845 GSA v1 (C2 build-38 BPM); train = replicate 3 (120 arrays), evaluate = replicates 1-2 (240 arrays)",
|
||||
"truth": "1000G NYGC 30x phased panel, chr22 SNVs on the array",
|
||||
"egt_v1_fixed_windows": {
|
||||
"chrom": "22",
|
||||
"samples": 240,
|
||||
"truth_sites": 8278,
|
||||
"call_rate": 0.9947053434807118,
|
||||
"concordance": 0.9926765907658587,
|
||||
"nrd": 0.018946074088334416
|
||||
},
|
||||
"egt_v2_bic_hwe": {
|
||||
"chrom": "22",
|
||||
"samples": 240,
|
||||
"truth_sites": 8278,
|
||||
"call_rate": 0.9960623540307643,
|
||||
"concordance": 0.9943676222304063,
|
||||
"nrd": 0.013034595450012981
|
||||
},
|
||||
"vendor_gsa_v1_c1_egt": {
|
||||
"chrom": "22",
|
||||
"samples": 240,
|
||||
"truth_sites": 8278,
|
||||
"call_rate": 0.9915201940887493,
|
||||
"concordance": 0.9945781643910259,
|
||||
"nrd": 0.012251034586575862
|
||||
}
|
||||
}
|
||||
Reference in new issue
Block a user