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== Imputation into Phased Haplotypes ==
== Imputation into Phased Haplotypes ==
Imputing genotypes using '''minimac''' is an easy straightforward process: after selecting a set of reference haplotypes, plugging-in the target haplotypes from the previous step and setting the number of rounds to use for the model parameter estimation, imputation should proceed rapidly.
Imputing genotypes using '''minimac''' is an easy and straightforward process: after selecting a set of reference haplotypes, plugging-in the target haplotypes from the previous step and setting the number of rounds to use for the model parameter estimation, imputation should proceed rapidly.
=== Running Minimac ===
=== Running Minimac ===
=== Reference Haplotypes ===
=== Reference Haplotypes ===
Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-08.html MaCH download page]. The most recent set of haplotypes are based on genotype calls from August 2010.
Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-08.html MaCH download page]. The most recent set of haplotypes are based on genotype calls from the August 2010 data freeze.
=== Imputation quality evaluation ===
=== Imputation quality evaluation ===
Minimac drops each of the genotyped SNPs in turn and then calculates 3 statistics:
To evaluate imputation quality, Minimac hides data for each genotyped SNP in turn and calculates 3 statistics:
* looRSQ - this is the estimated rsq for that SNP (as if SNP weren't typed).
* looRSQ - this is the estimated rsq for that SNP (as if SNP weren't typed).
* empR - this is the empirical correlation between true and imputed genotypes for the SNP. If this is negative, the SNP is probably flipped.
* empR - this is the empirical correlation between true and imputed genotypes for the SNP. If this is negative, the SNP is probably flipped.
* empRSQ - this is the actual R2 value, comparing imputed and true genotypes.
* empRSQ - this is the actual R2 value, comparing imputed and true genotypes.
These statistics can be found in the *.info file
These statistics can be found in the .info file
=== X Chromosome Imputation ===
=== X Chromosome Imputation ===
:::: '''<Example of a male only pedigree file >'''
:::: '''<Example of a male only pedigree file>'''
:::: FAM1003 ID1234 0 0 M A/0 A/0 C/0
:::: FAM1003 ID1234 0 0 M A/A A/A C/C
:::: FAM1004 ID5678 0 0 M 0/0 C/0 G/0
:::: FAM1004 ID5678 0 0 M 0/0 C/0 G/G
:::: ...
:::: ...
:::: '''<End of pedigree file>'''
:::: '''<End of pedigree file>'''
''Note that, consistent with the Merlin convention, hemizygous males are listed as if they were homozygous.''
:::: '''<Example of the corresponding haplotype file>'''
:::: '''<Example of the corresponding haplotype file>'''
:::: ...
:::: ...
:::: '''<End of the corresponding haplotype file>'''
:::: '''<End of the corresponding haplotype file>'''
= post-imputation association analysis =
= post-imputation association analysis =
