From Genome Analysis Wiki
Jump to navigationJump to search
613 bytes added
, 21:31, 13 December 2010
Line 176: |
Line 176: |
| | | |
| These statistics can be found in the *.info file | | 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. |
| + | |
| | | |
| = Related Pages = | | = Related Pages = |