Minimac3 files download

Minimac3 is a lower memory and more computationally efficient implementation of minimac2. It is an algorithm for genotypic imputation that works on phased genotypes and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.

This wiki page is designed to give users a detailed step-by-step description on running typical GWAS imputation experiments. This section gives a brief summary of the steps required to go through an experiment of imputation on typical GWAS samples. Before pre-phasing and imputation, users must ensure that their data is quality controlled. Standard quality control filters involve excluding markers with high missingness rate, high deviations from Hardy-Weinberg equilibrium, high discordance rates if duplicate copies available , excess Mendelian inconsistencies etc.

For versions earlier than 0. Minimac3 is a lower memory and more computationally efficient implementation of minimac2. It is an algorithm for genotypic imputation that works on phased genotypes say from MaCH and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. This wiki page is designed to give users a detailed explanation of the info file outputted by Minimac3.

The SNP identifier for the variant. This is usually in the form of chr:position , but could be the rsid of the variant if the user had selected --rsid during the Minimac3 run provided the input reference panel as the rsid in the INFO column.

The dosage value see Dosage in the. This is the allele frequency of alternate ALT allele in the imputed dosage data see Dosage.

This is the minor allele frequency of the variant in the imputed dosage data. This is the average probability certainty of observing the most likely allele for each haplotype. A negative correlation between imputed and experimental genotypes can indicate allele flips. This statistic also can only be provided for genotyped sites. EmpRsq is the square of this correlation. Minimac3 is available as an undocumented release version. There are a few pages in this Wiki that may be useful to for Minimac3 users.

Here are links to a few:. In case of any queries and bugs please contact Sayantan Das. Jump to: navigation , search. It accomplishes this by identifying repeat haplotype patterns and using these to simplify the underlying calculations, with no loss of accuracy. Minimac3 uses M3VCF files customized minimac3 VCF files to store reference panel information in a compact form, thus saving on memory and time required to read large datasets.

M3VCF files can also store pre-calculated estimates of recombination fraction and error, which speeds up later rounds of imputation. Minimac3 outputs results in the form of standard VCF files for easy data manipulation in downstream analysis. Minimac3 is currently available as a release version. Please join our NEW mailing list to get updates about future releases or report possible bugs or email them to Sayantan Das.

Github Repo: Users can clone from github repository as well : Minimac3 Github.