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
{
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"samples": 360,
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"min_qual": 10.0,
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"ignored_filters": [
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"SampleQuality"
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],
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"sensitivity": {
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"DEL": {
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"100-500kb": {
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"found": 230,
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"truth": 1554,
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"rate": 0.148
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},
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"1000-infkb": {
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"found": 0,
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"truth": 15,
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"rate": 0.0
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},
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"25-50kb": {
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"found": 54,
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"truth": 225,
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"rate": 0.24
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},
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"50-100kb": {
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"found": 132,
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"truth": 894,
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"rate": 0.1477
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},
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"500-1000kb": {
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"found": 51,
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"truth": 180,
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"rate": 0.2833
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}
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},
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"DUP": {
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"100-500kb": {
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"found": 279,
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"truth": 1059,
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"rate": 0.2635
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},
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"1000-infkb": {
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"found": 9,
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"truth": 21,
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"rate": 0.4286
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},
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"25-50kb": {
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"found": 4,
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"truth": 198,
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"rate": 0.0202
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},
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"50-100kb": {
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"found": 55,
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"truth": 462,
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"rate": 0.119
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},
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"500-1000kb": {
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"found": 19,
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"truth": 78,
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"rate": 0.2436
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}
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}
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},
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"precision": {
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"DEL": {
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"in_truth": 473,
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"calls": 1814,
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"rate": 0.2607
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},
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"DUP": {
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"in_truth": 367,
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"calls": 1494,
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"rate": 0.2456
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}
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},
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"replicate_reproducibility": {
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"CNV": {
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"matched": 2132,
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"comparisons": 6616,
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"rate": 0.3222
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},
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"LOH": {
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"matched": 400,
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"comparisons": 532,
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"rate": 0.7519
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}
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},
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"calls_per_sample_median": 6.0,
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"loh_calls_per_sample_median": 0.0
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} |