Changes

== 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).

# 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.