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When filling in missing values can be justified at all, the dosage should come from your variant caller or modern imputation software.) As alpha and beta testing continue, plink2 will become increasingly usable on its own, but for now it's better to think of it as a supplement to rather than a replacement for v1.9. Solaris is no longer explicitly supported, but it should be able to run the linux binaries Usually, if any old allele code doesn't line up with an allele code in the main dataset, the variant is skipped (and logged to plink2.allele.no.snp) If you are not using macos m1, then you need to download the corresponding plink 2 and 1.9 executables (minimum versions as above) for your system and rename them as plink2 and plink19 respectfully. File format reference this page describes specialized plink 2.0 input and output file formats which are identifiable by file extension