PRIMED file conversion workflows


This workflow uses plink2 to convert a file from binary PLINK format (bed/bim/fam) to VCF.

Default behavior is to output SNPs only, omitting any “I/D” codes for indels, as these are not accepted by downstream workflows such as liftover and imputation.

Any pseudoautomsomal SNPs (‘XY’ code) will be merged with the X chromosome using plink2’s “merge-x” option. The default is

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