readme.pregsf90
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readme.pregsf90 [2020/05/22 16:41] – [Quality Control (QC) for G] dani | readme.pregsf90 [2022/01/08 21:21] – [Output files for GWAS (postGSf90)] dani | ||
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Useful for check for Mendelian conflicts and HWE (with also '' | Useful for check for Mendelian conflicts and HWE (with also '' | ||
- | The //file// should | + | The //file// should |
//SNP_ID// - identification of the SNP (alphanumeric) \\ | //SNP_ID// - identification of the SNP (alphanumeric) \\ | ||
//CHR// - chromosome number (numeric), starting from 1 \\ | //CHR// - chromosome number (numeric), starting from 1 \\ | ||
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- | First SNP in the Map fiel corresponds to first SNP in genotype file, and so on. | + | The first SNP in the Map file corresponds to the first SNP in the genotype file, and so on. |
- | Other alphanumeric | + | Other alphanumeric |
If '' | If '' | ||
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< | < | ||
- | Check and remove | + | Check and provide a list of individuals with extreme high diagonals in the genomic relationship matrix.\\ |
If optional //x// is present set the threshold\\ | If optional //x// is present set the threshold\\ | ||
default value 1.6 | default value 1.6 | ||
< | < | ||
- | Check and remove | + | Check and provide a list of individuals with extreme low diagonals in the genomic relationship matrix.\\ |
If optional //x// is present set the threshold\\ | If optional //x// is present set the threshold\\ | ||
default value 0.7 | default value 0.7 | ||
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* 1: trait | * 1: trait | ||
* 2: effect | * 2: effect | ||
- | * 3: values of SNP effects to use in Manhattan plots | + | * 3: values of SNP effects to use in Manhattan plots [abs(SNP_i)/ |
* 4: SNP | * 4: SNP | ||
* 5: Chromosome | * 5: Chromosome | ||
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< | < | ||
- | contains | + | contains |
* 1: trait | * 1: trait |
readme.pregsf90.txt · Last modified: 2024/05/16 15:11 by dani