gwas
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
gwas [2020/06/22 17:13] trynke |
gwas [2020/06/22 17:21] trynke |
||
|---|---|---|---|
| Line 73: | Line 73: | ||
| * Unimputed: Genotypes determined on the basis of the SNP array, not imputed against genomic reference panels. | * Unimputed: Genotypes determined on the basis of the SNP array, not imputed against genomic reference panels. | ||
| - | ==== Non-Caucasian samples ==== | + | ===== Non-Caucasian samples ===== |
| To prevent false-positive association, non-Caucasian samples are excluded. | To prevent false-positive association, non-Caucasian samples are excluded. | ||
| Line 81: | Line 81: | ||
| * Population stratification (using Eigenstrat) | * Population stratification (using Eigenstrat) | ||
| - | ==== Cryptic relationships ==== | + | ===== Cryptic relationships ===== |
| Samples are selected using self reported family relations. After cleaning of the data, samples are compared with each other to determine the relationship by genetic similarity. If a pair of samples are indicated as first degree relatives, the sample with the best genotyping quality will be included. | Samples are selected using self reported family relations. After cleaning of the data, samples are compared with each other to determine the relationship by genetic similarity. If a pair of samples are indicated as first degree relatives, the sample with the best genotyping quality will be included. | ||
| Line 87: | Line 87: | ||
| ===== Releasing SNP genotype data ===== | ===== Releasing SNP genotype data ===== | ||
| The following files are available through the Lifelines workspace or HPC: | The following files are available through the Lifelines workspace or HPC: | ||
| - | • files with phenotype data | + | * files with phenotype data |
| - | + | * files with genotyped and imputed data | |
| - | • files with genotyped and imputed data | + | * quality control files: |
| - | + | * list of samples excluded | |
| - | • quality control files: | + | * list of SNPs excluded |
| - | -list of samples excluded | + | * PCA component file |
| - | -list of SNPs excluded | + | |
| - | -PCA component file | + | |
| ===== Abbreviations ===== | ===== Abbreviations ===== | ||
gwas.txt · Last modified: 2021/05/27 17:21 by trynke
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 4.0 International
