Changes

::::  '''<End of the corresponding haplotype file>'''

::::  '''<End of the corresponding haplotype file>'''

=== Imputation quality evaluation ===

== Imputation quality evaluation ==

Minimac hides each of the genotyped SNPs in turn and then calculates 3 statistics:

Minimac hides each of the genotyped SNPs in turn and then 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).  

These statistics can be found in the *.info file

These statistics can be found in the *.info file

Be aware that imputation quality statistics are not directly comparable between different imputation programs (MaCH/minimac vs. Impute vs. Beagle etc.).

Be aware that, unfortunately, imputation quality statistics are not directly comparable between different imputation programs (MaCH/minimac vs. Impute vs. Beagle etc.).

== Questions and Comments ==

== Questions and Comments ==

Please contact [mailto:goncalo@umich.edu Goncalo Abecasis] or [mailto:cfuchsb@umich.edu Christian Fuchsberger (minimac)] or [mailto:yunli@med.unc.edu Yun Li (MaCH)].

Please contact [mailto:goncalo@umich.edu Goncalo Abecasis] or [mailto:cfuchsb@umich.edu Christian Fuchsberger (minimac)] or [mailto:yunli@med.unc.edu Yun Li (MaCH)].