Changes

'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!

'''If you downloaded Minimac3 version earlier than 0.1.13 (can check the LOG file; source code downloaded before Oct 15, 2015 or imputed data downloaded from Imputation Server) please see this page for Info File descriptors. If using version 0.1.13 or above, please see [[Minimac3 Info File | new version of Minimac3 Info page]]''' !!!

  [There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to get the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency of the imputed data in the info file, while the minor and major alleles in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the minor allele frequency in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor allele in the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5).

'''[P.S There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file makes it easier for users to get the minor allele in the imputed data. In the earlier versions, we only reported the minor allele frequency of the imputed data in the info file, while the minor and major alleles in the info file were major/minor alleles with respect to the reference panel allele frequency and NOT imputed data allele frequency. As a result, the users only had the minor allele frequency in their info files but NO way of knowing which one was the minor allele in the imputed data (although most of the times we have the same major/minor allele in the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5).

 

= Introduction =

= Introduction =