This package is designed to align a PLINK fileset with a FASTA reference genome.
Flippy is a simple, fast script to ensure that PLINK filesets are aligned to a reference genome in FASTA format. It identifies and fixes strand flipping, and reversed alleles. It removes ambiguous (palindromic) alleles and sites that do not match the reference genome. It also recognizes and removes multi- allelic sites and indels by default. Instructions and more details can be found on GitHub.
