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183 bytes removed
, 18:05, 6 August 2012
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− | === 1. Split by sex === | + | === 1. Split the X chromosome pedigree file by sex === |
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− | # 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 |
− | ### 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 minimac as described above.
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| :::: ... | | :::: ... |
| :::: '''<End of the corresponding haplotype file>''' | | :::: '''<End of the corresponding haplotype file>''' |
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| === 2. Impute non-pseudo-autosomal part by sex === | | === 2. Impute non-pseudo-autosomal part by sex === |