kemal
a4c9c2d7d8
- qc/controls: canonical control names (QC-002), bkg/offset (QC-003), 13 genotyping metrics (QC-004/005), missing/zero-divisor handling (QC-007/008); controls_raw.tsv / controls_qc.tsv (QC-009/011) incl. compat CSVs - qc/thresholds + profiles: YAML schema, validation codes, precedence, shipped profiles, auto (QC-020..025) - qc/status: functional PASS/FAIL/NA, control CLEAR/FLAGGED, flags (QC-030..033) - qc/contamination: BAF regression; bit-compatible with gtc2vcf BAFregress (36/36, K-017), exact mode too - qc/relatedness: KING-robust, duplicates, Mendelian errors, pedigree from sheet (IN-018) - qc/locus_summary: OUT-072, bit-identical to BeadArrayFiles except ChiTest (K-018) - qc/suggest: suggest-thresholds (QC-026) - pipeline/qc: disk-backed cohort store; CLI qc controls|samples|contamination|relatedness|loci|suggest-thresholds - genotype: control tables (OUT-070), het_rate, QC columns, cohort QC - tests: unit + oracle (BAFregress plugin, BeadArrayFiles locus summary)
22 lines
548 B
YAML
22 lines
548 B
YAML
# Starting point for review, not a truth (spec QC-024): recalibrate on your own data with
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# `simurg qc suggest-thresholds`. For EX-format genotyping chips (provisional, OQ-046).
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qc:
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report:
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callRate: 0.98
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logRDev: 0.20
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stainingGreen: 5
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stainingRed: 5
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extensionGreen: 5
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extensionRed: 5
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hybGreenHighMed: 1
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hybGreenMediumLow: 1
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targetRemovalI: 1
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restoration: null
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stringency: 2
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nonSpecificBindingGreen: 1
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nonSpecificBindingRed: 1
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npGreen: 5
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npRed: 5
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assayControl: 1
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bgOffset: 3000
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