kemal
a5728d84e3
GSE165845 360 arrays: constitutional DEL/DUP calls 77/74 % in the NYGC SV truth, LOH reproduced across replicates 74 %; mosaic calls are mostly false positives (12-23 %), sensitivity for 25 kb-1 Mb events 7-13 % at QUAL >= 20. All samples had been flagged SampleQuality by the summary logr_dev (cluster-file mismatch); the gate now uses the SD of the LRR after the batch reference. Validation script: --ignore-filter.
89 lines
1.3 KiB
JSON
89 lines
1.3 KiB
JSON
{
|
|
"samples": 360,
|
|
"min_qual": 20.0,
|
|
"ignored_filters": [
|
|
"SampleQuality"
|
|
],
|
|
"sensitivity": {
|
|
"DEL": {
|
|
"100-500kb": {
|
|
"found": 126,
|
|
"truth": 1554,
|
|
"rate": 0.0811
|
|
},
|
|
"1000-infkb": {
|
|
"found": 0,
|
|
"truth": 15,
|
|
"rate": 0.0
|
|
},
|
|
"25-50kb": {
|
|
"found": 16,
|
|
"truth": 225,
|
|
"rate": 0.0711
|
|
},
|
|
"50-100kb": {
|
|
"found": 70,
|
|
"truth": 894,
|
|
"rate": 0.0783
|
|
},
|
|
"500-1000kb": {
|
|
"found": 13,
|
|
"truth": 180,
|
|
"rate": 0.0722
|
|
}
|
|
},
|
|
"DUP": {
|
|
"100-500kb": {
|
|
"found": 117,
|
|
"truth": 1059,
|
|
"rate": 0.1105
|
|
},
|
|
"1000-infkb": {
|
|
"found": 6,
|
|
"truth": 21,
|
|
"rate": 0.2857
|
|
},
|
|
"25-50kb": {
|
|
"found": 1,
|
|
"truth": 198,
|
|
"rate": 0.0051
|
|
},
|
|
"50-100kb": {
|
|
"found": 15,
|
|
"truth": 462,
|
|
"rate": 0.0325
|
|
},
|
|
"500-1000kb": {
|
|
"found": 10,
|
|
"truth": 78,
|
|
"rate": 0.1282
|
|
}
|
|
}
|
|
},
|
|
"precision": {
|
|
"DEL": {
|
|
"in_truth": 222,
|
|
"calls": 571,
|
|
"rate": 0.3888
|
|
},
|
|
"DUP": {
|
|
"in_truth": 149,
|
|
"calls": 436,
|
|
"rate": 0.3417
|
|
}
|
|
},
|
|
"replicate_reproducibility": {
|
|
"CNV": {
|
|
"matched": 554,
|
|
"comparisons": 2014,
|
|
"rate": 0.2751
|
|
},
|
|
"LOH": {
|
|
"matched": 286,
|
|
"comparisons": 394,
|
|
"rate": 0.7259
|
|
}
|
|
},
|
|
"calls_per_sample_median": 2.0,
|
|
"loh_calls_per_sample_median": 0.0
|
|
} |