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]]''' !!!

['''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 determine the minor allele in their imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported 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 MAF of their imputed data 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 alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. '''For users with this earlier version of info file, there is NO need to re-run the imputation.''' If you need to determine the minor allele in your imputed data, you just need to calculate the MAF on your side. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries we have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates.

['''P.S.''' There is NO analytical difference between the two versions of the info file. The new version of the Minimac3 info file just makes it easier for users to determine the minor allele in their imputed data. In the earlier versions, we only reported the minor allele frequency (MAF) of the imputed data in the info file, while the minor and major alleles reported 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 MAF of their imputed data 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 alleles between the reference and GWAS data, sometimes the alleles get swapped, especially when the MAF is close to 0.5). In the new version, we report the REF and ALT alleles and the ALT allele frequency along with MAF; thus comparing the MAF with the alternate allele frequency, one can easily determine the minor allele in the their imputed data. '''For users with this earlier version of info file, there is NO need to re-run the imputation.''' The imputed data is same. Only the info files have slightly different formats. And if you need to determine the minor allele in your imputed data, you just need to calculate the MAF on your side from the imputed data. Please contact [mailto:sayantan@umich.edu Sayantan Das] for any queries you have. We, the authors of Minimac3, apologize for any inconvenience caused due to these updates.

= Introduction =

= Introduction =