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Minimac

613 bytes added, 20:31, 13 December 2010
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These statistics can be found in the *.info file
 
=== X Chromosome Imputation ===
minimac supports the imputation of genotypes on the X chromosome (non-pseudo-autosomal part).
 
# 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
### Remove the pseudo-autosomal part (for build hg18: chrX:1-2709520 and chrX:154584238-154913754 ; for build hg19 chrX:1-2709520 and chrX:154584238-154913754 )
### Convert the pedigree file in a MaCH haplotype file (missing genotypes should be encoded as: '0' or '.' or 'N' )
### Impute using minimac as described above.
 
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