integrarray_qc_guidelines
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| integrarray_qc_guidelines [2025/12/15 23:09] – [Molecular validation of findings.] 98.60.169.32 | integrarray_qc_guidelines [2026/01/23 21:20] (current) – Added Files 206.192.168.19 | ||
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| ==== 1. Genotype Calling ==== | ==== 1. Genotype Calling ==== | ||
| - | Genotypes were called for many samples at the Center for Inherited Disease Research (CIDR). The genotyping platform used was the Global Screening Plus Custom Array (here called the GSA array but also referenced as product by BPM Amos_Custom_20032937X382854_A1, | + | Genotypes were called for many samples at the Center for Inherited Disease Research (CIDR). The genotyping platform used was the Global Screening Plus Custom Array (here called the GSA array but also referenced as product by BPM Amos_Custom_20032937X382854_A1, |
| ===== 2. Sample QC ===== | ===== 2. Sample QC ===== | ||
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| - | No samples were dropped; all samples will be included in the imputation. | + | No samples were dropped; all samples will be included in the imputation, the marker lists of all steps can be found in file: {{ : |
| * **735,370** markers in the original release (chr1–chr23) | * **735,370** markers in the original release (chr1–chr23) | ||
| - | * **942** markers with ≥3 discordant calls among 149 duplicate pairs | + | * **942** markers with ≥3 discordant calls among 149 duplicate pairs, missing genotypes were not included |
| - | * **3,552** markers with p < 1×10⁻⁷ in controls | + | * **3,552** markers with p < 1×10⁻⁷ in 14,537 unrelated caucasian |
| - | * **2,052** markers with p < 1×10⁻¹² in cases | + | * **2,052** markers with p < 1×10⁻¹² in 9895 unrelated caucasian |
| * **23,112** markers with call rate < 0.95 | * **23,112** markers with call rate < 0.95 | ||
| - | * **27,119** total unique markers affected by filters | + | * **27,119** total unique markers affected by filters |
| * **708,672** markers remaining after removing the filtered markers | * **708,672** markers remaining after removing the filtered markers | ||
| - | * **615,894** markers retained after running the McCarthy Group Tool workflow against the TOPMed R3 reference panel | + | * **632,677** markers retained after running the McCarthy Group Tool workflow against the TOPMed R3 reference panel |
integrarray_qc_guidelines.1765840180.txt.gz · Last modified: by 98.60.169.32