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Revision as of 18:05, 6 August 2012
, 18:05, 6 August 2012→1. Split by sex
=== 1. Split by sex ===
=== 1. 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 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.
:::: ...
:::: ...
:::: '''<End of the corresponding haplotype file>'''
:::: '''<End of the corresponding haplotype file>'''
=== 2. Impute non-pseudo-autosomal part by sex ===
=== 2. Impute non-pseudo-autosomal part by sex ===
