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381 bytes added, 21:37, 13 December 2010
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### 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 into a MaCH haplotype file (missing genotypes should be encoded as: "0" or "." or "N" )
'''<Example of a pedigree file >'''
FAM1003 ID1234 0 0 M A/0 A/0 C/0
FAM1004 ID5678 0 0 M 0/0 C/0 G/0
'''<End of pedigree file>'''
'''<Example of a phased haplotype file>'''
FAM1003->ID1234 HAPLO1 AAC
FAM1003->ID1234 HAPLO2 AAC
FAM1004->ID5678 HAPLO1 0CG
FAM1004->ID5678 HAPLO2 0CG
'''<End of phased haplotype file>'''
### Impute using minimac as described above.

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