primed-file-conversion
PRIMED file conversion workflows
plink2_bed2vcf
This workflow uses plink2 to convert a file from binary PLINK format (bed/bim/fam) to VCF.
Inputs:
| input | description |
|---|---|
| bed_file | plink bed file |
| bim_file | plink bim file |
| fam_file | plink fam file |
| fasta_file | (optional) fasta file. If provided, plink2 attempts to assign ref and alt alleles according to the reference genome. |
| out_prefix | (optional) prefix for outp |
This is a companion discussion topic for the original entry at github.com/UW-GAC/primed-file-conversion/liftover_vcf