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
This is a companion discussion topic for the original entry at github.com/UW-GAC/primed-file-conversion/plink2_vcf2pgen