Hi Chris,
Would you be able to add a flag to filter out palindromic SNPs in Plink 1.9 and 2?
Like --flip, it might be useful to add a 'permissive' option to retain non-SNP variants.
Also there would be corner cases when a variant is monomorphic in a ped/map file, so when imported to later Plink versions the second allele is 0. I guess those should be allowed to remain.
Thanks,
Kaustubh.