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Minimac: 1000 Genomes Imputation Cookbook

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