integrarray_qc_guidelines
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| integrarray_qc_guidelines [2025/12/15 19:32] – Figure inserted 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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| Overall PCA for independent markers: | Overall PCA for independent markers: | ||
| + | {{ : | ||
| The QC steps prior to imputation were refined based on Chris’ suggestions. | The QC steps prior to imputation were refined based on Chris’ suggestions. | ||
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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: {{ : |
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| - | · 735,370 markers in the original release (chr1–chr23) | + | |
| - | + | ||
| - | · 942 markers with ≥3 discordant calls among 149 duplicate pairs | + | |
| - | + | ||
| - | · 3,552 markers with p < 1×10⁻⁷ | + | |
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| - | · 2,052 markers with p < 1×10⁻¹² in cases | + | |
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| - | · 23,112 markers with call rate < 0.95 | + | |
| - | + | ||
| - | · 27,119 total unique markers affected by filters (3), (4), (5), and (6) | + | |
| - | · 708,672 markers remaining after removing the filtered markers | + | * **735,370** markers in the original release (chr1–chr23) |
| + | * **942** markers with ≥3 discordant calls among 149 duplicate pairs, missing genotypes were not included | ||
| + | * **3,552** markers with p < 1×10⁻⁷ in 14,537 unrelated caucasian controls | ||
| + | * **2,052** markers with p < 1×10⁻¹² in 9895 unrelated caucasian cases | ||
| + | * **23,112** markers with call rate < 0.95 | ||
| + | * **27,119** total unique markers affected by filters discordant calls, HWE and call rate | ||
| + | * **708,672** markers remaining after removing the filtered markers | ||
| + | * **632,677** markers retained after running the McCarthy Group Tool workflow against the TOPMed R3 reference panel | ||
| - | · 615,894 markers retained after running the McCarthy Group Tool workflow against the TOPMed R3 reference panel | ||
integrarray_qc_guidelines.1765827172.txt.gz · Last modified: by 98.60.169.32