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Revision as of 18:22, 10 February 2011
, 18:22, 10 February 2011no edit summary
| 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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=== X Chromosome Imputation ===
=== X Chromosome Imputation ===
=== 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
