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3 bytes added
, 02:33, 16 September 2014
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| == X Chromosome Imputation == | | == X Chromosome Imputation == |
− | minimac supports the imputation of genotypes on the X chromosome (non-pseudo-autosomal part).
| + | minimac2 supports the imputation of genotypes on the X chromosome (non-pseudo-autosomal part). |
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| # Split the X chromosome pedigree file by sex. | | # Split the X chromosome pedigree file by sex. |
− | ## 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 minimac2). |
| ## For males | | ## For males |
| ### Remove the pseudo-autosomal part (for build hg18: chrX:1-2709520 and chrX:154584238-154913754 ; for build hg19 chrX:60001-2699520 and chrX:154931044-155260560) | | ### Remove the pseudo-autosomal part (for build hg18: chrX:1-2709520 and chrX:154584238-154913754 ; for build hg19 chrX:60001-2699520 and chrX:154931044-155260560) |
− | ### 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 minimac2 as described above. |
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