Differences

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--- integrarray_qc_guidelines [2025/12/15 19:32] – Figure inserted 98.60.169.32
+++ integrarray_qc_guidelines [2025/12/23 16:14] (current) – [Molecular validation of findings.] 206.192.168.19
@@ Line 171: / Line 171: @@
 Overall PCA for independent markers:
+{{ :31949_ind_pc1_vs_pc2.png?500 |}}
 The QC steps prior to imputation were refined based on Chris’ suggestions.
@@ Line 182: / Line 182: @@
-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: {{ :integrarray_qc_guidelines_marker_list.xlsx |}}
-· 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 in controls
-· 2,052 markers with p < 1×10⁻¹² in cases
-· 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