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70 bytes added
, 18:08, 6 August 2012
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| === 1. Split the X chromosome pedigree file by sex === | | === 1. Split the X chromosome pedigree file by sex === |
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| # For females: follow the same protocol as for autosomes (phase with MaCH and impute with minimac). | | # For females: follow the same protocol as for autosomes (phase with MaCH and impute with minimac). |
| # For males | | # For males |
| ## Convert the pedigree file into a MaCH haplotype file (missing genotypes should be encoded as: "0" or "." or "N" ) and impute using minimac as described above. | | ## Convert the pedigree file into a MaCH haplotype file (missing genotypes should be encoded as: "0" or "." or "N" ) and impute using minimac as described above. |
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| === 2. Impute non-pseudo-autosomal part by sex === | | === 2. Impute non-pseudo-autosomal part by sex === |
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| + | Impute females and males separately |
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| === 3. Impute pseudo-autosomal part by sex === | | === 3. Impute pseudo-autosomal part by sex === |
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| + | Impute females and males separately |
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| == Imputation quality evaluation == | | == Imputation quality evaluation == |