kemal
80b93e9f45
- Omni2.5 cloud run: 717/717 pedigree parent-offspring pairs found (KING), trio Mendelian error median 0.031 %, sex vs pedigree 99.6 %, P4 preset re-check 2138/2141 byte-identical (K-015 closed) - qc/controls: skip bead addresses absent from the IDAT; control missing only if none is on the chip - QC-008 amended: signal / zero background = +Inf (passes), 0/0 = NaN (flagged); Inf in TSV/report - plotly bundle stored gzip-compressed (repo grep stays clean: the DOM event name contains the forbidden substring) - docs: validation P5 part 2, summaries, known_unknowns K-021
133 lines
3.3 KiB
JSON
133 lines
3.3 KiB
JSON
{
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"n_gtc": 2141,
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"n_compared": 2141,
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"errors": [],
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"byte_identical": 2138,
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"samples_with_no_field_diff": 2138,
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"samples_with_field_diff": {
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"raw_x": 1,
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"genotypes": 3,
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"genotype_scores": 3,
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"base_calls": 3,
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"call_rate": 2,
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"logr_dev": 3,
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"raw_y": 2,
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"normalization_transforms": 2
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},
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"genotype_diff_loci_total": 5,
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"score_diff_loci_total": 18229,
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"max_score_abs_diff": 0.9426311254501343,
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"cluster_files": [
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"HumanOmni2.5-4v1-Multi_B.egt"
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],
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"sex_agreement_by_version": {
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"1": 2141,
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"2": 2129
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},
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"ref_sex_counts": {
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"M": 1054,
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"F": 1087,
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"U": 0
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},
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"examples": [
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{
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"gtc": "/work/omni/data/5767788121/5767788121_R01C01.gtc",
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"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
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"max_score_abs_diff": 0.6647092700004578,
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"field_diffs": {
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"genotypes": 1,
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"genotype_scores": 1,
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"base_calls": 1,
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"call_rate": [
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"0.9905122518539429",
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"0.9905126690864563"
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],
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"logr_dev": [
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"0.16615425050258636",
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"0.16615475714206696"
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]
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},
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"sex_by_version": {
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"1": "F",
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"2": "F"
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},
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"sex_ref": "F",
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"byte_identical": false,
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"ref_layout_canonical": true,
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"metadata": {
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"autocall_version": "1.6.2.2",
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"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
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"imaging_date": "Wednesday, September 07, 2011 11:17:40 PM"
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}
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},
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{
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"gtc": "/work/omni/data/5826354152/5826354152_R02C01.gtc",
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"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
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"genotype_scores": 4270,
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"0.9955130815505981",
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"0.9955138564109802"
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],
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"logr_dev": [
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"0.16252823173999786",
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"0.16252586245536804"
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]
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},
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"sex_by_version": {
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"1": "M",
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"2": "M"
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},
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"sex_ref": "M",
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"byte_identical": false,
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"ref_layout_canonical": true,
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"metadata": {
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"autocall_version": "1.6.2.2",
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"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
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"imaging_date": "Wednesday, September 07, 2011 10:41:50 PM"
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}
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},
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{
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"gtc": "/work/omni/data/6268201099/6268201099_R02C01.gtc",
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"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
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"max_score_abs_diff": 0.37550604343414307,
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"field_diffs": {
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"genotypes": 2,
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"genotype_scores": 13958,
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"base_calls": 2,
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"normalization_transforms": true,
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"logr_dev": [
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"0.18736381828784943",
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"0.18737195432186127"
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]
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},
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"sex_by_version": {
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"1": "F",
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"2": "F"
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},
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"sex_ref": "F",
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"byte_identical": false,
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"ref_layout_canonical": true,
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"metadata": {
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"autocall_version": "1.6.2.2",
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"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
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"imaging_date": "Wednesday, October 19, 2011 1:41:11 AM"
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}
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}
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],
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"params": {
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"preset": "autocall-1.6.2",
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"norm_version": "1.1.2",
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"sex_version": 1
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},
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"seconds": 1101.9,
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"passed": false
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}
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