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4 bytes removed
, 18:22, 10 February 2011
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| | Reduce memory use at the cost of approximately doubling runtime. This option is recommended for most GWAS scale datasets and computing platforms. | | | Reduce memory use at the cost of approximately doubling runtime. This option is recommended for most GWAS scale datasets and computing platforms. |
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− | === Imputation quality evaluation ===
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− | Minimac drops each of the genotyped SNPs in turn and then calculates 3 statistics:
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− | * looRSQ - this is the estimated rsq for that SNP (as if SNP weren't typed).
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− | * empR - this is the empirical correlation between true and imputed genotypes for the SNP. If this is negative, the SNP is probably flipped.
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− | * empRSQ - this is the actual R2 value, comparing imputed and true genotypes.
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− | These statistics can be found in the *.info file
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| === X Chromosome Imputation === | | === X Chromosome Imputation === |
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| + | === Imputation quality evaluation === |
| + | Minimac drops each of the genotyped SNPs in turn and then calculates 3 statistics: |
| + | * looRSQ - this is the estimated rsq for that SNP (as if SNP weren't typed). |
| + | * empR - this is the empirical correlation between true and imputed genotypes for the SNP. If this is negative, the SNP is probably flipped. |
| + | * empRSQ - this is the actual R2 value, comparing imputed and true genotypes. |
| + | |
| + | These statistics can be found in the *.info file |
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