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The handle <code>--processReference</code> is used to ONLY convert reference panels from <code>VCF</code> format to [[#M3VCF Files|<font face=Courier>M3VCF</font>]] format (and save parameter estimates). NO imputation will be performed and thus NO target/gwas haplotypes are required. However, by default, parameter estimation will be done using the reference panel and the estimates will be saved in the <code>M3VCF</code> files. Users should use <code>--rounds 0</code> in order to opt out of parameter estimation and only compress the reference panel and save it as a <code>M3VCF</code> file. See [[#Examples|examples]] and the [[#List of Options|list of options]] below for further details.
The handle <code>--processReference</code> is used to ONLY convert reference panels from <code>VCF</code> format to [[#M3VCF Files|<font face=Courier>M3VCF</font>]] format (and save parameter estimates). NO imputation will be performed and thus NO target/gwas haplotypes are required. However, by default, parameter estimation will be done using the reference panel and the estimates will be saved in the <code>M3VCF</code> files. Users should use <code>--rounds 0</code> in order to opt out of parameter estimation and only compress the reference panel and save it as a <code>M3VCF</code> file. See [[#Examples|examples]] and the [[#List of Options|list of options]] below for further details.
[NOTE: If parameter estimates are found in M3VCF files, Minimac3 will automatically use them for imputation. Users should use handle <code>--updateModel</code> in order to update the parameters using the target/gwas panel as well. However, this is NOT necessary in most cases unless the user has strong reason to believe that this might increase the imputation accuracy.
[NOTE: If parameter estimates are found in <code>M3VCF</code> files, Minimac3 will automatically use them for imputation. Users should use handle <code>--updateModel</code> in order to update the parameter estimates using the target/gwas panel as well. However, this is NOT necessary in most cases, unless the user has strong reasons to believe that this might increase the imputation accuracy.]
= Examples =
= Examples =
